MtoZ Biolabs

Boston, United States

Protein analysis is a fundamental step in studying biological systems, and it is essential in various fields such as drug development, disease diagnosis, and agricultural breeding. At MtoZ Biolabs, we provide comprehensive protein analysis services using advanced mass spectrometry techniques combined with our expertise in proteomics. With the aim of advancing your research and maximizing your success, our protein analysis services are designed to be reliable, efficient, and precise.

Services at MtoZ Biolabs

Our protein analysis service is based on state-of-the-art mass spectrometry, including LC-MS/MS and MALDI-TOF/TOF. We utilize these technologies to identify and quantify proteins in biological samples. The proteins are first separated by HPLC and then ionized before being introduced into the mass spectrometer. The mass-to-charge ratios of the ions are measured to determine the molecular weight of the proteins. By comparing the obtained mass spectra to a database of known protein sequences, we can identify the proteins present in your sample.

Applications

Our protein analysis service can be applied in various fields, including but not limited to:

• Biomedical research: Identifying and quantifying proteins involved in diseases can help understand the disease mechanism and develop potential therapeutic targets.
• Drug development: Our service can assist in the discovery and validation of drug targets, as well as in the evaluation of drug efficacy.
• Agricultural breeding: Protein analysis can help to understand the genetic traits of crops and livestock, promoting the breeding of high-quality varieties.

Sample Submission Requirements

For successful protein analysis, please ensure your samples meet our submission requirements:

• Samples should be clear without visible impurities.
• The protein concentration should be higher than 1mg/mL.
• Ensure your samples are stored and shipped under appropriate conditions to prevent protein degradation.

At MtoZ Biolabs, we are committed to providing our clients with the most reliable and highest quality protein analysis service. Please feel free to contact us if you have any questions about our service.

About Us

MtoZ Biolabs is an integrate contract research organization (CRO) providing advanced proteomics, metabolomics, bioinformatics, and biopharmaceutical analysis services to researchers in biochemistry, biotechnology, and biopharmaceutical fields. The name of MtoZ represents mass to charge ratio in mass spectrometry analysis, as most of our services are provided based on our well-established mass spectrometry platforms. Our services allow for the rapid and efficient development of research projects, including protein analysis, proteomics, and metabolomics programs.

MtoZ Biolabs is specialized in quantitative multiplexed proteomics and metabolomics applications through the establishment of state-of-the-art mass spectrometry platforms, coupled with high-performance liquid chromatography technology. We are committed to developing efficient, and effective tools for addressing core bioinformatics problems. With a continuing focus on quality, MtoZ Biolabs is well equipped to help you with your needs in proteomics, metabolomics, bioinformatics, and biopharmaceutical research. Our ultimate aim is to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample.

Email: marketing@mtoz-biolabs.com

In recent years, the use and number of biotherapeutics has increased significantly. For these protein-based therapies, the quantitation of aggregates is of particular concern, given their potential effect on efficacy and immunogenicity. This need has renewed interest in size-exclusion chromatography (SEC). SEC is a chromatographic method, which acts as a sieve and separates molecules in solution by their size, and in some cases molecular weight. Molecular sieves are materials containing precise and single tiny holes, which can be used to adsorb gases or liquids. SEC has long residence time for small molecular weight compounds into gel pores, whereas large molecular compounds are washed away earlier. The advantage of molecular sieve chromatography is that it can efficiently process at least 1nmol of target protein. The separation time is also very short, generally within 3 hours, and the chromatographic separation peak obtained at the same time is also smaller.

Advantages of SEC in Protein Purification

1. The buffer solution used for SEC can be exchanged and desalted.

2. Similar varieties (such as protein fragments and oligomers) can be separated.

3. Compatible with a variety of solvents.

4. Independent on any particular form of protein for preservation and elution.

The liquid chromatography is divided into positive and reverse phase chromatography according to the relative polarity of the mobile phase and the stationary phase. Reversed-phase liquid chromatography (RPLC) refers to chromatographic method that uses a hydrophobic stationary phase. RPLC has the characteristics of high resolution and high repeatability, therefore it has been widely used in protein and polypeptide analysis, esp. for the separation of small molecular weight proteins and protein fragments with molecular weight

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is a technology commonly used in protein purification and analysis. SDS-PAGE can separate proteins according to the differences in the charge and the different mobility due to different molecular sizes. If the protein sample has been highly purified and contains only one protein, the results would show a single protein band after SDS-PAGE separation. However, when there are multiple proteins in the protein samples, different proteins can be separated into multiple protein bands through SDS-PAGE. Therefore, SDS-PAGE technology provides a direct way to analyze the purity of protein samples. To meet the research needs of analyzing the purity of protein products, MtoZ Biolabs has developed and optimized a SDS-PAGE based workflow, and provides an accurate analytical service for protein/peptide purification study.

Analytical Principles of SDS-PAGE

SDS is a type of anionic surfactant that can break the hydrogen and hydrophobic bonds in proteins. SDS can bind to proteins in a certain proportion to form SDS-protein complexes, covering the intrinsic charges of proteins. Therefore, the migration speed of all kinds of SDS-protein complexes is only determined by the molecular weight of proteins. Different proteins are separated by SDS-PAGE electrophoresis, followed by protein staining and analysis of protein bands.

Reports

Experiment procedures

Parameters of SDS-PAGE

Protein purity results

Bioinformatics analysis

About Us

MtoZ Biolabs is an integrated Contract Research Organization (CRO) dedicated to providing cutting-edge chromatography and mass spectrometry services for researchers in biochemistry, biotechnology, and biopharmaceutical fields. Our team of experts and advanced technological platforms are designed to support your research projects with precision and reliability.

Email: marketing@mtoz-biolabs.com

MtoZ Biolabs uses LC-MS for antibody C-terminal variation analysis, including detection of the proportion of K deletion in the C-terminal end of antibody and other types of truncation on antibody C-terminal.

Disulfide bond is essential for protein molecules to maintain the correct advanced structure and maintain protein bioactivity. The distribution of disulfide bonds in antibody drugs is a direct structural characteristic of the drugs. Therefore, confirmation of disulfide bonds plays a very important role in the confirmation process of antibody drug structure. MtoZ Biolabs has developed a high-resolution mass spectrometry, coupled with pLink-SS software, to provide our customers with accurate analysis of disulfide bonds and free cysteines. Our sample preparation steps have also been optimized to prevent in vitro exchange of disulfide bonds, and maintain native structure.

Application of Disulfide Bond Analysis

(1) Identification of the number of disulfide bonds in the biopharmaceuticals and free cysteines

Glycosylation, especially N-glycosylation, is a universal post-translational modification in regarding the localization, function, activity of proteins in tissues and cells. Among the information related to N-glycosylation, the site of N- glycosylation is the basis for our understanding of its sugar chain function. Besides the application of point mutation in traditional biochemistry, the study of glycosylation sites has also played an important role in the identification of glycosylation sites in N-terminal. MALDI TOF MS and nano LC-ESI-MS/MS are commonly used to identify the N/O-glycosylation sites in the antibodies. MtoZ Biolabs uses both MALDI TOF MS and nano LC-ESI-MS/MS technology to provide efficient and accurate glycosylation analysis of multiple biopharmaceuticals, including proteins, antibodies, etc.

Ideally, any technology for detecting Host Cell Protein (HCP) should: (i) detect protein concentrations across a wide dynamic range, from extremely low concentrations of individual impurity proteins to much higher concentrations of impurity proteins; (ii) track changes in HCP populations and concentrations throughout the entire bioprocess; (iii) simultaneously monitor and measure multiple protein analytes; and (iv) monitor and measure low concentration HCP even in the presence of target recombinant protein at high concentrations. Additionally, if a risk-based assessment of HCP is necessary, these methods should be capable of identifying HCP at any stage of the bioprocess. Employing anti-HCP antibodies for qualitative and quantitative detection and removal of HCPs is highly effective. Thus, the development of anti-HCP antibodies is of significant importance.

1. Identification of HCP Antigens

A variety of cell lines, including mammalian, insect, plant, and prokaryotic cells such as Escherichia coli, are employed for producing recombinant proteins for therapeutic purposes. Chinese hamster ovary cells (CHO) are widely used in the biotechnology industry. For instance, pIs range from 3-11, with molecular weights from 5kDa to 250kDa for large proteins. During the purification process, the content of the product protein gradually increases, while the content of host impurity proteins significantly decreases, dropping from >10-90% to.

About Us

MtoZ Biolabs is an integrated Contract Research Organization (CRO) dedicated to providing cutting-edge chromatography and mass spectrometry services for researchers in biochemistry, biotechnology, and biopharmaceutical fields. Our team of experts and advanced technological platforms are designed to support your research projects with precision and reliability.

Email: marketing@mtoz-biolabs.com

AQUA absolute quantitative analysis is a targeted quantitative proteomics technique widely used in various quantitative proteomics studies. The absolute quantification strategy can be used for the absolute quantification of proteins and their modified states. By using stable isotope-labeled synthetic peptides as internal standards, it can simulate the natural peptides formed by protein hydrolysis, and can also be prepared using covalent modifications (such as phosphorylation, methylation, acetylation, etc.). By using selected reaction monitoring (SRM) analysis in MS/MS, AQUA internal standard peptides are used for precise quantitative determination of the absolute levels of proteins and post-translationally modified proteins after protein hydrolysis. MtoZ Biolabs provides integrate Absolute Quantitative Analysis (AQUA) Service.

The advancement of MS technology has promoted the development of large-scale quantitative analysis methods for intracellular protein expression levels.

Analysis Workflow

Figure 1. Analysis Workflow of AQUA

Protein absolute quantification strategy is an effective detection method for protein quantification and post-translational modifications. Absolute quantification is achieved by using synthetic peptides labeled with stable isotopes: based on discovering the relationship between mass spectrometry signal and protein concentration, the average mass spectrometry signal response of the three strongest trypsin peptides per mole of protein is constant, with a coefficient of variation less than 10%. As long as a given internal standard (a synthetic peptide containing isotopic labels) is provided, the relationship between mass spectrometry signal and protein concentration can be used to determine a universal signal response factor (counts/mol). The universal signal response factors for all quantified proteins are the same.

The absolute quantification method relies on the use of synthetic internal standard peptides, which are introduced into the cell lysate at a known concentration during the digestion process. During the detection process in a tandem mass spectrometer, the hydrolyzed protein samples are analyzed by the SRM method, allowing for direct detection and quantification of natural peptides and isotopically labeled AQUA internal standard peptides. This method's simplicity and sensitivity, combined with the widespread use of tandem mass spectrometers, make the AQUA absolute quantification strategy an effective method for directly measuring protein levels and post-translational modifications from cell lysates.

The process where proteins separated by electrophoresis are transferred or blotted from the gel matrix onto a membrane (usually nitrocellulose or polyvinylidene difluoride (PVDF)), followed by subsequent antibody-based detection on the membrane surface, is known as western blot (WB) or immunoblotting. Mtoz Biolabs provides WB analysis services. Through highly selective and sensitive antibody-antigen interactions, WB can be used to detect specific target proteins from complex protein mixtures, such as tissue homogenates or cell extracts. The obtained data can be used for qualitative and semi-quantitative analysis of target proteins. MtoZ Biolabs provides integrate Protein Immunoblotting and Electrotransfer Services.

Analysis Workflow

Figure 1. General Flowchart of Electric Transfer

WB is a widely used protein analysis technique for detecting specific proteins in tissue homogenates or extract samples. It uses gel electrophoresis to separate native proteins and denatured proteins by their 3D structures and peptide chain lengths, respectively. After separation, the proteins are transferred onto a membrane, where specific antibodies recognize the target proteins specifically. WB is widely applied in molecular biology, biochemistry, immunogenetics, and other molecular biology fields.

In WB analysis, proteins are first separated from gel electrophoresis by various methods such as SDS-PAGE and IEF, by isoelectric point (pI), molecular weight, charge, or a combination of these factors. SDS-PAGE is commonly used for separation because all proteins are dissolved within the gel and migrate in the same direction, and the denaturing effect of SDS makes antigenic epitopes more easily recognizable.

After gel electrophoresis analysis, proteins are transferred from the gel to a membrane made of nitrocellulose or PVDF for antibody detection. PVDF membranes have higher protein binding capacity than nitrocellulose membranes, but nitrocellulose membranes are better at binding smaller proteins. The main method of transferring proteins is electroblotting, which uses electricity to pull proteins from the gel into the PVDF or nitrocellulose membrane. Electrophoretic transfer methods include wet transfer, semi-dry transfer, and semi-wet transfer. If protein separation is done by IEF, then using pressure transfer diffusion to transfer proteins is more effective.

The transfer process varies from one hour (semi-dry transfer) to overnight transfer (wet transfer). After the transfer is complete, the free binding sites on the membrane are blocked by the protein mixture, thus subsequent antibody detection is not interfered. The proteins transferred to the membrane can then undergo antibody detection. Membranes containing proteins are first incubated with primary antibodies, followed by detection with secondary antibodies that recognize the primary antibodies. Secondary antibodies generally carry a reporter group and have high sensitivity.

The most sensitive detection method is using enhanced chemiluminescence (ECL): recognizing primary antibodies with an antibody-horseradish conjugate. Using special variants of ECL, protein bands as low as 1 pg can be detected.

WB can also be used to track the phosphorylation of proteins, with antibodies that bind to all subtypes of phosphorylated proteins presenting a bead-like appearance on 2D gels. It can also be used to identify known and unknown proteins in complexes produced by IP, as long as the target proteins are in the gel, they can be identified by coomassie brilliant blue staining, .

Multiple reaction monitoring (MRM) is a targeted quantitative proteomics research method for target protein. MRM, based on information about the target molecule, selectively chooses data for mass spectrometry data collection, collecting signals that meet the criteria of target ions and eliminating that of ions that do not meet the criteria. MRM mass spectrometry analysis goes through three stages: 1) filtering out parent ions consistent with the specificity of the target molecule through MS; 2) colliding and fragmenting these parent ions to eliminate interference from other ions; 3) collecting mass spectrometric signals from selected specific MS/MS2 ions only. MRM mass spectrometry technology is a high-precision protein quantification technique and is an excellent method for one-time precise quantification of multiple target proteins in complex samples. If isotope-labeled target peptides are used as internal references, absolute quantification of proteins can be achieved. MtoZ Biolabs provides integrate MRM/PRM Quantitative Proteomics Service.

MtoZ Biolabs utilizes AB SCIEX TripleTOF 5600, AB SCIEX Triple Quad 5500, Q Exactive, and Fusion mass spectrometry platforms combined with Nano-LC, launching MRM/PRM targeted quantitative proteomics analysis service. You just need to provide us with the information about the target proteins you need to study, and we provide a one-stop MRM quantitative proteomics analysis service. It includes establishing and optimizing MRM methods, selecting specific peptides, labelling peptides by isotope, analyzing by mass spectrometry, analyzing raw data, and analyzing by bioinformatics method.

Experimental Instruments

AB SCIEX TripleTOF 5600, AB SCIEX Triple Quad 5500, Q Exactive, Fusion

Analysis Workflow

Service Advantages

High sensitivity, selecting of ions consistent with the target ions by two-stage mass spectrometry and excluding interfering ions to greatly enhance the signal-to-noise ratio and improve the accuracy of detected target ions.High throughput, the number of protein identified can reach up to 200 at once.Capablility of absolute quantitative analysis without antibodies.High-precision identification of low-abundance proteins and quantitative range across four orders of magnitude.

Applications

Application of MRM Technology

(1) Result validation of label-free and other non-targeted proteomics.

(2) Simultaneous absolute quantification study of multiple proteins/peptides.

(3) Study the change of protein families with high homology but lacking specific recognition antibodies.

(4) Quantitative study of post-translational modifications of proteins.

(5) Absolute quantification study of biological disease targets.

Application of SRM/MRM

(1) Verification of iTRAQ differential proteins.

(2) Verification of label-free differential protein post-products.

(3) Absolute quantification of peptides and proteins.

(4) Quantification of disease markers and establishment of diagnostic models.

(5) Quantification of phosphorylated proteins and methylated proteins.

(6) Quantification of other post-translational modifications protein.

(7) Quantitative analysis of pathway .

Sample Submission Requirements

Deliverables

MRM Spectrum Analysis and Protein Data Quality AssessmentPCA of Multi-component SamplesIdentified Protein Functional Annotation: GO Functional Annotation, KEGG Functional Annotation and COG Functional AnnotationDifferential Protein Expression Statistical Analysis: Venn Diagrams and Volcano PlotsDifferential Protein Expression Clustering Analysis:.

4D-DIA quantitative proteomics is an emerging high-throughput mass spectrometry technology that combines data-independent acquisition (DIA) strategies with four-dimensional (4D) separation techniques. It involves digesting protein into peptide by protease and separating peptide by liquid chromatography (LC), followed by mass spectrometry (MS) for detection and identification of peptide. It enables high-throughput and high-sensitivity quantitative analysis of proteins in biological samples. 4D-DIA is widely used in fields such as biomedicine research, disease diagnosis, and drug development. Its in-depth analysis of proteome helps reveal biological process, discover potential biomarker, and study drug targets to promote scientific research and clinical applications. MtoZ Biolabs provides integrate 4D-DIA Quantitative Proteomics Service.

Analysis Workflow

Sample Preparation

Proteins extraction from biological samples, followed by purification and concentration.

Protein Digestion

Protein digestion with enzymes (such as trypsin) to produce peptides.

Peptide Separation

Peptides separation by high-performance liquid chromatography (HPLC).

Mass Spectrometry Analysis

4D-DIA analysis of separated peptides by mass spectrometer, including their retention time (RT), mass-to-charge ratio (m/z), ion intensity, and ion mobility, followed by mass spectrometry data collection and mass spectrum match.

Data Processing and Quantitative Analysis

Identification of peptide and quantification of protein by searching for mass spectrometry databases.

Service Advantages

High Throughput

4D-DIA technology can analyze a large number of samples simultaneously, significantly reducing experimental cycle and improving experimental efficiency.

High Accuracy

4D-DIA technology uses high-sensitivity, high-resolution mass spectrometers for protein quantification, offering high accuracy and reliability and avoiding error and omission.

Comprehensive Coverage

4D-DIA technology can analyze almost all proteins in samples, not just specific ones.

Data Reproducibility

The data generated by 4D-DIA technology have high repeatability and reproducibility, ensuring the stability and credibility of experimental results.

Applications

Functional Proteomics Research

Exploration of the structure, function, and interactions of proteins, providing a critical theoretical foundation for biological science.

Protein Modification Research

Modifications of protein can affect its function and regulatory roles. 4D-DIA quantitative proteomics is used to study various types of protein modifications, such as protein phosphorylation, protein acetylation, protein methylation, etc.

Disease Biomarker Identification

Identification of potential disease biomarkers by comparing pathological samples with normal samples, enhancing the accuracy of early diagnosis and efficacy of disease treatment.

New Drug Development

In-depth research on the mechanisms of drug action to develope more targeted medications and offer personalized treatments.

Sample Submission Requirements

We accept a variety of samples, including cell samples, tissue samples, body fluid samples (such as serum, plasma, urine, saliva, etc.), and microorganism samples (such as bacteria, viruses, fungi, etc.).

Service atMtoZ labs

Experimental ProceduresRelevant Mass Spectrometry ParametersDetailed Information on 4D-DIA Quantitative ProteomicsMass Spectrometry ImagesRaw Data

With the increasing focus on personalized healthcare, there is a growing demand for biomarkers for early diagnosis, prognosis, patient stratification, or monitoring treatment response. Compared with genetic biomarkers, protein biomarkers provide higher degrees of differential information. Olink proteomics is based on a unique proximity extension assay (PEA) technique that enables simultaneous quantification of multiple protein biomarkers. Olink PEA uses 2 matching antibodies for each target antigen. Each antibody pair is labeled with a unique DNA oligonucleotide barcode. When antibodies bind to the same target protein in solution, the DNA oligochain will anneal to sufficient stability to achieve DNA elongation. Then the DNA barcode is amplified and the amplicons obtained through qPCR or next-generation sequencing (NGS) is measured for absolute or relative quantification. PEA can detect protein with high sensitivity. Mtoz Biolabs provides integrate Olink Analysis Service.

Olink proteomics provides high-throughput solutions for protein biomarker discovery, enabling the detection of numerous proteins in biological samples with concentration low to microscale, and its analytical methods are rigorously validated, which can provide superior specificity at multiple levels. Due to its high sensitivity and high throughput, Olink proteomics has been widely used in the fields of biomarker discovery, disease mechanism research, drug development and personalized healthcare. In clinical biomarker research, it can be used in all stages of drug development, including early detection and preclinical and clinical development.

Analysis Workflow

Minimum Clinical Sample Concentration (Plasma/Serum as Low as 1 L)High Sensitivity to Protein Detection, Similar to ELISA or BetterImproved Accuracy of Multiple Detection and Intermediate Multiple Detection (with the Average Internal Coefficient of Variation (%CV) Lower than 10% and the Average Intermediate Coefficient of Variation (%CV) Lower than 20%)More than 10 Logarithms of the Dynamic Range Which Is Ideal for Study of Plasma Protein GroupHigh Specificity of Protein Detection Aouble Recognition of Two Antibodies and Unique DNA Barcode of each Protein without Cross-reactivityvailablethrough D

Applications

Drug Target Identification

(1) Identify protein quantitative trait loci (pQTLs) to link genetic variations, proteins, and diseases.

(2) Delve into tumor biology, immune regulation mechanism, phenotypic change, and the transition from cold tumor to hot tumor.

Biomarker Analysis and Screening

Analyze longitudinal biomarker data between early and late time points to identify key biomarkers related to the transition from drug sensitivity to drug resistance.

Protein Response Validation in Clinical Trials

(1) Predict and monitor therapeutic response, sensitivity, and immune resistance mechanism.

(2) Guide strategies to optimize response rates and identify new target pathways.

Exploratory Endpoints in Clinical Trials

(1) Explore the correlation between circulating protein biomarker and clinical outcome.

(2) Predict the onset and mechanisms of treatment-related toxicity and monitor cytokine release syndrome and neurotoxicity.

(3) Predict relapse and treatment progression in adjunct therapy.

Deliverables

In the results report, MtoZ Biolabs will provide you with a detailed results report, which includes:

Experimental ProceduresAbsolute Quantification Data (pg/mL) (Limited to Olink Target 48)Relative Quantification Data: Expressed in Normalized Protein Expression.

Peptidomics refers to the study of all endogenous bioactive peptides in organism, cell, or tissue. Bioactive peptides are biologically active substances involved in various cellular functions within organism, which include cytokines, growth hormones, and disease-specific degradation fragments of certain proteins in body fluid. These peptides play a crucial role in the regulation of organism, encompassing hormone regulation, neurotransmitter modulation, cell growth and proliferation, and immune modulation. The investigation of peptide structures and physiological functions holds significant importance in life sciences. Peptidomics is the discipline that studies the structure and function of the peptidome from multiple perspectives. Mass spectrometry (MS) employed in peptidomics enable both qualitative and quantitative identification of peptide in samples. MtoZ Biolabs provides integrate Peptidomics Analysis Service.

Service at MtoZ Biolabs

Peptide Purity AnalysisPeptidomics AnalysisPeptide Biomarker IdentificationPeptide Mass Spectrometry IdentificationHigh-accuracy MS-based Immunopeptidomics Analysis and Neoantigen DiscoveryPeptide Structure Determination

High performance liquid chromatography (HPLC) is a modern chromatographic separation technique extensively utilized in biological, chemical, and medical research. For peptide purity analysis, HPLC identifies the composition and content of peptides in samples, assessing the purity and impurities. Peptides are dissolved in a mobile phase and separated using a chromatographic column containing a stationary phase. Different components in the peptide sample exhibit distinct retention times based on their interactions. The detector analyzes retention time and signal intensity to qualitatively and quantitatively assess peptide purity. MtoZ Biolabs provides integrate HPLC Peptide Purity Analysis Service.

Analysis Workflow

Sample Preparation

Dissolve peptide samples in an appropriate solvent (e.g., water, acetonitrile, methanol) to form the test solution.

Set HPLC Conditions

Adjust parameters like mobile phase, flow rate, gradient program, and detection wavelength according to sample characteristics and the chromatographic column.

System Equilibration

Flow the mobile phase through the column until reaching a stable equilibrium to ensure reproducible results.

Sample Injection

Introduce the test solution to the chromatography system using an automatic or manual injector.

Separation Process

Peptide samples are carried through the column by the mobile phase, separating components based on their interaction with the stationary phase.

Detection and Data Collection

The detector sequentially registers each peptide component passing through, producing electrical signals. The system captures retention time and signal intensity to create chromatograms.

Data Processing and Analysis

Specialized software processes chromatograms, providing qualitative and quantitative peptide purity analysis based on retention time and signal intensity.

Drug Development and Preparation

Assess peptide drug purity, composition, impurities, and concentration to ensure drug quality and safety while enabling high-purity peptide preparation.

Industrial Production

Monitor purification steps, degradation, and impurity production during peptide manufacturing to guide process optimization and quality control.

Clinical Diagnosis

Measure peptide levels in biological samples (e.g., serum, urine) to support clinical diagnosis, disease monitoring, and treatment evaluation.

Food Safety

Confirm peptide additive and residue purity in food, ensuring safety and quality.

Environmental Monitoring

Detect peptide pollutants in environmental samples (e.g., water, soil) to aid environmental risk assessment and pollution control.

Sample Submission Requirements

In the technical report, MtoZ Biolabs will provide you with a detailed technical information, including:

Experimental ProceduresRelevant Chromatographic ParametersHPLC Peptide Purity Analysis Detailed InformationChromatography ImagesRaw Data

Peptides are abundant in living organisms, actively participating in key biological processes such as hormone regulation, enzyme catalysis, and immune responses. Their spatial structure and functional features greatly influence their biological activity. Accurately determining peptide structures is essential for understanding peptide folding patterns, bioactivity, and structural features. It also informs drug development and bioengineering optimization. Peptide structure determination is valuable in biomedical research and drug development, providing insight into protein structure-function relationships, supporting drug design, and advancing vaccine research. Furthermore, it is critical in studying disease mechanisms, developing protein-based drugs, and refining biotechnology applications. MtoZ Biolabs provides integrate Peptide Structure Determination Service.

Analysis Workflow

Sample Preparation

Extract and purify target peptides using high-performance liquid chromatography (HPLC) or other suitable techniques. Desalt and concentrate purified peptides to meet structural analysis requirements.

Sequence Analysis

(1) Select appropriate enzymes to digest peptide samples based on sequence characteristics, producing fragments for mass spectrometry analysis.

(2) Use HPLC to separate enzymatically cleaved peptides.

(3) Determine peptide fragments' amino acid composition and sequence via Edman degradation or tandem mass spectrometry (MS/MS), revealing the primary peptide structure.

Structural Analysis

Measure the peptides ultraviolet absorption by circular dichroism (CD), identifying their internal secondary structure elements such as -helices and -folds.

Revealing Protein Structure

Peptide structure determination identifies protein structures, including secondary, tertiary, and quaternary structures.

Studying Protein Function

Since protein structure closely correlates with function, peptide structure determination illuminates these relationships.

New Drug Development

By identifying drug-target protein interactions, peptide structure determination provides crucial insights for drug design.

Disease Diagnosis and Treatment

Peptide structure determination helps identify disease-specific biomarkers, enhancing early diagnosis and treatment efficacy.

Deliverables

In the technical report, MtoZ Biolabs will provide you with a detailed technical information, including:

Experimental ProceduresRelevant Mass Spectrometry ParametersPeptide Structure Determination Detailed InformationMass Spectrometry ImagesRaw Data

The immunopeptidome comprises all short peptides presented on the cell surface by HLA-I and II molecules for T-cell recognition. Immunopeptidomics analysis aims to explore the dynamics and composition of both type I and II immune peptides. Comprehensive characterization of the immunopeptidome aids in developing new therapies for cancer, immune diseases, and infectious diseases. MtoZ Biolabs provides integrate Immunopeptidomics Service.

Immune peptides are the complete set of peptides presented by nucleated cells through type I and II proteins within the HLA or MHC antigen presentation pathways. They are essential in defining immunogenic epitopes during immune responses. Characterizing these immune peptides can help identify targets for personalized cancer immunotherapies, including neoantigens arising from tumor-specific mutations or tumor-associated antigens. Moreover, this knowledge facilitates the development of novel mRNA and peptide vaccines and cell-based therapies.

MtoZ Biolabs offers a comprehensive high-resolution mass spectrometry-based immunopeptidomics analysis and neoantigen discovery solution, including proprietary, highly sensitive immune peptide enrichment and identification protocols. Our approach helps identify over 10, 000 type I and over 10, 000 type II peptides. Using our optimized high-throughput platform, immunopeptidomics analysis enables reliable identification and quantification from minimal samples. This service supports large-scale studies, empowering researchers to uncover solutions for cancer, immune diseases, and infectious diseases and identify unexplored therapeutic targets.

Services at MtoZ Biolabs

MtoZ Biolabs' comprehensive neoantigen discovery solution offers peptide synthesis, functional screening of neoantigen candidates for personalized cancer vaccines and T-cell therapies, animal testing of personalized cancer vaccines, and clinical-stage vaccine immunogenicity trials.

Deliverables

A Comprehensive List of All Identified Immune Peptides, Neoantigen Peptides, and Tumor-Associated Antigen PeptidesImmunopeptidome Data Quality Analysis Reports, as Presented in Case Studies

Sample Submission Requirements

Biomarkers are measurable traits that serve as indicators of normal biological activities, disease processes, or pharmacological responses to therapeutic interventions. Peptides are particularly suitable as biomarkers due to their ability to circulate among various body compartments. Many disease processes can be inferred from the characteristic peptide profiles and pathological changes observed in different body fluids. Moreover, variations in peptide abundance associated with various diseases are detectable. MtoZ Biolabs provides integrate Peptide Biomarker Discovery & Validation Service.

Two prevalent approaches to developing peptide biomarkers are pattern recognition and single/oligo biomarker assay. Pattern recognition does not require identifying the candidate biomarkers and relies solely on mass spectrometry's exceptional specificity and sensitivity to derive patient information. In contrast, the single/oligo biomarker assay is more effective as their expression levels can be verified across various biological samples. Mass spectrometry-based methods can accurately determine analyte concentrations and feature precise mass measurement and sequencing capabilities.

Figure 1. Peptide Biomarkers Analysis

To screen and validate peptide biomarkers, it is necessary to identify the peptides in a sample (qualitative analysis) and quantify their concentrations (quantitative analysis). Effective screening requires integrating both steps. Numerous analytical techniques are employed in biomarker detection, among which the combination of mass spectrometry and liquid chromatography (e.g., UPLC and nanoLC) stands out for its high resolution, sensitivity, throughput, and quantification capabilities.

MtoZ Biolabs employs the Thermo Fishers Orbitrap Fusion Lumos mass spectrometry system along with nanoLC chromatography for advanced peptide biomarkers analysis services.

Peptides, structurally akin to proteins, are molecules composed of amino acid sequences. They play pivotal roles in regulating blood pressure, modulating pain perception, and managing glucose metabolism, yet are significantly smaller than proteins. Endogenous peptides typically arise from the cleavage of precursor proteins by various enzymes. Research into the collective peptide expression under specific physiological conditions is termed peptidomics. MtoZ Biolabs provides integrate Mass Spectrometry-Based Peptide Identification Service.

Peptide identification aims to achieve "Peptide-Spectrum Matches" by analyzing peptide sequence information to ascertain sequences or post-translational modifications. Tandem mass spectrometry, extensively employed in peptide identification, combines with bioinformatics for peptide sequencing in proteomics. This involves matching experimental spectral data against theoretical data from protein databases. A current focus of research is matching proteins with unknown sequences to database entries.

Analysis Workflow

Services at MtoZ Biolabs

Peptide Extraction from Test MaterialsChromatographic Separation of PeptidesPrimary Mass Spectrometric Analysis of Ionized Peptides Mass-to-Charge RatiosSecondary Mass Spectrometric Analysis of Fragmented Peptide IonsBioinformatics Analysis

Gel sealing in plastic film or gel strips in sealed tubes. Maintain moisture in sealed samples without excessive water or buffer.

Considerations

Mandatory Glove Use for Gel CuttingCleanliness of Cutting BladesPrecision in Cutting Gel Strips to Minimize Background NoiseStringent Avoidance of Keratin Contamination from Handling and Environmental Exposure

Deliverables

In the technical report, MtoZ Biolabs will provide you with detailed technical information, including:

Experimental ProceduresMass Spectrometry ParametersMass Spectrometry ImagesRaw DataDetailed Information of Identified Proteins

Peptide purity is defined as the ratio of the target peptide to all analytes, essentially reflecting the proportion of the target peptide to impurities. It is typically determined using HPLC analysis at 220nm, the peak absorption wavelength for peptide bonds. The purity of peptides critically influences research outcomes, with potential contaminants arising during chemical synthesis, culturing, or the extraction and purification phases. Impurities may include peptides with incomplete sequences, truncated sequences, incompletely deprotected peptides, and by-products from synthesis or final cleavage processes. MtoZ Biolabs provides integrate Peptide Purity Analysis Service.

Applications

Services at MtoZ Biolabs

RP-HPLC

Chromatograms from reverse phase HPLC are utilized to assess peptide purity by quantifying the peak area of the fully purified peptide relative to the total detected peak areas, facilitating the determination of by-product quantities and proportions.

Mass Spectrometry

Chromatograms from RP-HPLC are utilized to assess peptide purity by quantifying the peak area of the fully purified peptide relative to the total detected peak areas, facilitating the determination of by-product quantities and proportions.

Amino Acid Analysis (AAA)

Determines the amino acid composition in peptide or protein products, ensuring experimental accuracy and consistency.

MtoZ Biolabs delivers peptide purity analysis services leveraging RP-HPLC and mass spectrometry, dedicated to high-quality results. Each project requires a unique approach, so please engage our technical team to discuss specific needs.

The objective of peptidomics analysis extends beyond identifying and verifying all endogenous peptides in the biological samples under study. It also involves comparing the expression levels of target peptides across specific biochemical processes. Mass spectrometry facilitates a comprehensive analysis of these peptides. MtoZ Biolabs provides integrate Peptidomics Service.

Peptidomics and proteomics have similar strategic approaches in research; however, notable differences exist. In peptidomics, to accurately identify native peptides, including those with post-translational modifications, specific digestive enzymes are generally avoided. This enables direct identification through primary MS and secondary MS.

Advancements in MS/MS sequencing have increasingly supplanted the traditional Edman degradation technique for peptide identification. Mass spectrometry has become pivotal for identifying peptides in various tissue extracts, including bioactive peptides. Size exclusion chromatography (SEC) is employed to remove most proteins from biological samples, body fluids, and tissue extracts, thereby enhancing the precision and repeatability of LC-MS in peptide identification. MtoZ Biolabs offers tailored peptidomics analysis services to meet specific customer requirements.

In cell biology and biochemistry, post-translational modifications (PTMs) critically influence the stability, activity, localization, and functions of proteins. Among these, lactylation stands out as a significant PTM. This modification can occur on any protein residue with a free amino group, such as lysine, arginine, and tyrosine. During this process, lactate reacts with these amino acids to form an ester linkage, thereby altering protein structure and function. This change impacts several biological processes, including cell signaling, gene expression, and metabolism. Accurate identification and characterization of lactylation sites are essential for understanding their biological implications and for the development of related applications.MtoZ Biolabs provides integrate Protein Lactylation Modification Analysis Service.

Mass spectrometry is crucial for identifying lactylated proteins and studying their properties. This technique allows for precise determination of lactylation sites and explores the modification's impact on protein structure and function. Additionally, mass spectrometry is also used to screen for new lactylation sites, providing deeper insights into protein lactylation studies. Moreover, research on lactylation modification has a broad application value, including but not limited to understanding the structure and function of proteins, studying the pathogenesis of diseases, and the development of novel drugs, and helping us understand the complexity and dynamics of biological systems.

Figure 1. Mass Spectrometric Analysis of Protein Lactylation Modification

At MtoZ Biolabs, using the latest Thermo's Obitrap Exploris 240 mass spectrometer in combination with Nano-LC technology, we have developed a precise analytical platform for protein lactylation. This platform is adept at pinpointing lactylation sites and assessing their dynamic changes under various conditions, thereby revealing their effects on protein structure and function. Whether you aim to investigate the fundamental mechanisms of lactylation or its role in disease progression, MtoZ Biolabs offers comprehensive, efficient, and tailored analytical solutions. Contact us for more information on our protein lactylation modification analysis services.

Analysis Workflow

Protein Sample Preparation

Extract proteins from biological samples.

Protein Digestion

Digest proteins into smaller peptides using enzymes like trypsin or chymotrypsin.

Liquid Chromatography Separation

Further separate enriched peptides via high-performance liquid chromatography.

Peptide Enrichment

Enrich lactylated peptides using techniques like antibody enrichment or specific solid phase extraction.

Mass Spectrometric Analysis

Determine peptide masses and their fragmentation patterns to identify amino acid sequences, lactylation sites, and obtain quantitative data.

Angel, T. E. et. al. Chem. Soc. Rev. 2012.

Figure 2. Lactylation Modification Analysis Process

Service Advantages

Sensitivity and Accuracy

Detect lactylation modifications with high precision even at low abundances.

Localization of Modification Sites

Identify lactylation on proteins and precisely determine the affected amino acid residues.

Quantitative Capabilities

Assess the relative or absolute abundance of lactylation modifications to understand their biological impacts.

High-throughput Capability

Identify and quantify numerous lactylation sites in a single experiment.

Compatibility

Combine with other techniques like immunoprecipitation and bioinformatics for more comprehensive analyses.

Deliverables

Protein deamidation involves the conversion of amide groups (-CONH2) in amino acids like glutamic acid and aspartic acid into their corresponding acids, -ketoglutarate and glutamic acid, by losing an ammonia molecule (NH3). This non-enzymatic post-translational modification is crucial for understanding proteins' charge distributions, functions, stability, and interactions with other molecules, as well as their roles in diseases. For example, -amyloid proteins associated with Alzheimer's disease may become more prone to forming fibrils post-deamidation. Advances in molecular biology and mass spectrometry now allow for detailed analysis of such modifications. Using mass spectrometry, researchers can pinpoint exactly where deamidation occurs within protein sequences, which is essential for exploring protein functions, structures, and interactions. MtoZ Biolabs provides integrate Protein Deamidation Modification Analysis Service.

Figure 1. Protein Deamidation Modification Process

Protein deamidation analysis via mass spectrometry is a sophisticated approach in protein research. This method involves inducing deamidation through specific enzymes or chemicals, converting aspartic and glutamic acids' carboxyl groups into amine groups. This change reduces the mass of these amino acids by about 1Da, creating distinct mass-to-charge ratios detectable in mass spectrometry. This differential allows for the precise identification and quantification of deamidation modifications in proteins. MtoZ Biolabs offers a high-resolution mass spectrometry-based platform for this analysis, ensuring high-quality, comprehensive services for studying cellular signaling, protein interactions, and disease mechanisms.

Deliverables

In the technical report, MtoZ Biolabs will provide you with detailed technical information, including:

Experimental ProceduresRelevant Experimental ParametersDetailed Information on Protein Deamidation ModificationsMass Spectrometry ImagesRaw Data

Protein phosphorylation is a reversible post-translational modification where amino acid residues in proteins are phosphorylated by kinases, which attach covalently bonded phosphate groups. This modification alters proteins' conformation, potentially activating, deactivating, or changing their functions. Research into protein phosphorylation enhances our understanding of biological processes and helps to define the mechanisms of diseases linked to abnormal phosphorylation levels. Due to the low concentration and broad dynamic range of phosphorylated proteins in biological samples, enrichment of phosphorylated peptides is essential before performing quantitative proteomics to increase the detectability of these modifications. MtoZ Biolabs provides integrate Multipathway Phosphoproteomics Service.

MtoZ Biolabs employs the Multi-Pathway Enrichment Kit from CST company, along with Thermo Fisher's Orbitrap Fusion Lumos mass spectrometer and nanoLC, to offer comprehensive services in multipath protein phosphorylation proteomics. Clients need only specify their research goals and submit their samples; MtoZ Biolabs manages all subsequent steps including protein extraction, digestion, phosphorylated peptide enrichment, peptide separation, mass spectrometric analysis, analysis of raw data, and bioinformatics.

Analysis Workflow

Sample Submission Requirements

For Tissue Samples

Ship on dry ice; minimum requirements are 200 mg for plant tissues, 1 mL for blood (plasma should be anticoagulated with EDTA), 0.5 mL for serum, 2 mL for urine, 1 g for animal tissues, and 5*107 cells for cell samples. Yeast and microorganisms should have a dry weight of 200 mg.

For Protein Samples

Ensure a minimum of 1 mg total protein. Use standard lysis solutions for tissue and cell extraction.

Sample Shipping

Transport samples with adequate dry ice and opt for expedited shipping to minimize degradation risks during transit.

Sample Testing

We evaluate all samples before commencing the actual experiments. Testing must confirm sample integrity before proceeding with formal analyses.

Methylation represents one of the most prevalent post-translational modifications, chiefly affecting transcription factors and histones, though it also modifies a subset of cytoplasmic proteins. This modification includes monomethylation, symmetric/asymmetric dimethylation, and trimethylation on arginine (R) and lysine (K) residues. Arginine methylation plays critical roles in RNA processing, gene transcription, DNA damage repair, protein translocation, and signal transduction, whereas lysine methylation primarily influences histone function and epigenetic regulation of gene transcription. Targeted enrichment of methylated peptides using modification-specific antibodies, followed by LC-MS/MS analysis, facilitates extensive quantitative and qualitative assessment of protein methylation. MtoZ Biolabs provides integrate Quantitative Methylomics Service.

MtoZ Biolabs employs the Orbitrap Fusion Lumos mass spectrometer and nanoLC from Thermo Fisher for comprehensive protein methylation identification services. Clients need only submit their experimental aims and samples; MtoZ Biolabs handles all subsequent steps, including protein extraction, digestion, methylation specific peptide enrichment, peptide separation, mass spectrometric analysis, analysis of raw data, and bioinformatics.

Analysis Workflow

Plant Tissues (roots, xylem, phloem): > 5 g

Animal Tissues: > 200 mg wet weight

Microorganisms: > 2 g wet weight

Body Fluids (saliva, amniotic fluid, CSF): > 10 mL

Serum: > 500 L

Urine: > 50 L

Protein Extracts: > 2 mg/mL concentration, minimum total 1 mg, free of interfering substances like nucleic acids, lipids, and polysaccharides.

For Tissue Samples

Ship on dry ice.

For Protein Samples

Use standard lysis solutions for tissue and cell extraction.

Sample Shipping

Transport samples with adequate dry ice and opt for expedited shipping to minimize degradation risks during transit.

Sample Testing

We evaluate all samples before commencing the actual experiments. Testing must confirm sample integrity before proceeding with formal analyses.

Our team, seasoned in protocol optimization, ensures top-quality results in protein methylation studies. For specific inquiries, please contact us directly.

Service Advantages

High-Throughput

Capability to identify and quantify thousands of proteins simultaneously.

Complete Coverage

Digestion with 2-3 enzymes guarantees comprehensive protein analysis.

Applicability to Low-Abundance Methylated ProteinsState-of-the-Art Equipment

The Orbitrap Fusion Lumos, noted for its superior resolution and sensitivity.

Services at MtoZ Biolabs

Ion ChromatographyHigh Performance Liquid Chromatography (HPLC)Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS)

Deliverables

In the technical report, MtoZ Biolabs will provide you with detailed technical information, including:

Experimental ProceduresRelevant Mass Spectrometry ParametersDetailed Information on Identified Methylation SitesMass Spectrometry ImagesRaw Data

Protein oxidative modifications are generally induced by reactive oxygen species (ROS) such as superoxide anions, hydrogen peroxide, and hydroxyl radicals. These ROS are generated through multiple pathways in living organisms, including mitochondrial respiration, enzymatic redox reactions, and exposure to radiation. While protein oxidative modification is a natural physiological process, excessive ROS production or insufficient removal can cause excessive oxidation, impairing protein function and potentially leading to cellular damage. MtoZ Biolabs provides integrate Protein Oxidative Modification Analysis Service.

Advancements in molecular biology and biochemistry have positioned proteomics mass spectrometry as the primary method for investigating protein oxidative modifications. This technique allows for the precise identification of oxidatively modified amino acid residues and their chemical structures, facilitating detailed exploration into the types and mechanisms of these modifications. Employing mass spectrometry enables high-throughput screening and quantitative analysis of protein modification sites, offering crucial insights into cellular oxidative stress responses and the mechanisms underlying associated diseases.

Figure 1. Proteomic Oxidative Modification Mass Spectrometric Analysis

MtoZ Biolabs utilizes the Thermos Obitrap Fusion Lumos mass spectrometer in conjunction with Nano-LC technology to perform highly accurate analysis of protein oxidative modifications. This approach supports both quantitative and qualitative assessments, providing detailed information on modification types and locations. We accept a variety of protein samples and provide tailored one-stop solutions to meet diverse research needs. Free project evaluation!

Deliverables

In the technical report, MtoZ Biolabs will provide you with detailed technical information, including:

Experimental ProceduresRelevant Experimental ParametersDetailed Information on Protein Oxidative ModificationsMass Spectrometry ImagesRaw Data

Small ubiquitin-like modifier (SUMO) is a post-translational modification of proteins that refers to the covalent attachment of a small ubiquitin-associated modifier to a protein. Unlike ubiquitination, which targets proteins for degradation, sumoylation modulates protein function across several cellular processes including nucleocytoplasmic transport, transcription regulation, apoptosis, protein stability, stress response, and cell cycle progression. Despite low amino acid sequence similarity between SUMO and ubiquitin, they share very similar structural folds. SUMOs are about 100 amino acids in length, with variations in sequence length and mass among different family members and organisms. MtoZ Biolabs provides integrate Protein Sumoylation Identification Service.

Sumoylation is pivotal in controlling the subcellular localization of various proteins. Depending on the specific protein, sumoylation can occur in either the cytoplasm or nucleus. For instance, sumoylation can regulate the transport of the ribonucleoprotein RanGAP1 within the nuclear pore complex (NPC). Additionally, sumoylation affects the transcription process, as the activity of several transcription factors depends on their interaction with promyelocytic leukemia (PML) bodies and nuclear bodies (NBs), which require the sumoylation of PML protein for their assembly. Moreover, sumoylation plays a crucial role in chromosome congression and kinetochore assembly. If the function of SUMO-1 is abnormal, it can disrupt the correct distribution of chromatin during replication.

Figure 1. Protein Sumoylation Identification

MtoZ Biolabs leverages the Thermo Fisher's Orbitrap Fusion Lumos mass spectrometry platform, coupled with nanoLC-MS/MS chromatography, to deliver a comprehensive protein sumoylation analysis service. Clients are invited to submit their experimental objectives and samples, and our team will manage all aspects of the project thereafter.

Analysis Workflow

Protein Digestion in Gel or SolutionEnrichment of Sumoylated Proteins Through Antibodies Specific to Sumoylation MotifsHPLC Separation Followed by ESI-TOF MS/MS AnalysisAnalysis of Mass Spectrometry Data

Functional Annotation and Enrichment AnalysisCluster AnalysisNetwork AnalysisStatistical AnalysisAnalysis of Post-Translational Modification in Proteomics

Acylation is a post-translational modification involving the attachment of acyl groups, such as acyl-CoA, to proteins. This modification plays a pivotal role in regulating key biological processes including epigenetics, energy metabolism, protein trafficking, and molecular interactions. Acylation research is a dynamic field in life sciences, with studies expanding beyond acetylation to include propionylation, malonylation, glutarylation, succinylation, and crotonylation. Quantitative proteomics of acylation provides insights into the vital link between protein acylation changes and biological functions, offering valuable information for uncovering life mechanisms, identifying clinical disease markers, and targeting drug discovery. MtoZ Biolabs provides integrate Quantitative Acetylomics Service.

The acylation quantitative proteomics process begins by enzymatically digesting protein samples into peptides. These peptides are then separated using liquid chromatography to simplify the mixture. Specific acylation modifications are enriched using targeted antibodies or kits, followed by quantification with LC-MS/MS.

MtoZ Biolabs employs the Thermo Fishers Orbitrap Fusion Lumos mass spectrometry system alongside nanoLC platform for comprehensive acylation quantitative proteomics services. We invite researchers to share their experimental goals and submit their samples, after which our team manages all aspects of the analysis. This includes protein extraction, digestion, peptide enrichment, chromatographic separation, mass spectrometric analysis, and subsequent bioinformatics evaluations.

Sample Submission Requirements

For Tissue Samples

Ship on dry ice.

For Protein Samples

Use standard lysis solutions for tissue and cell extraction.

Sample Shipping

Transport samples with adequate dry ice and opt for expedited shipping to minimize degradation risks during transit.

Sample Testing

We evaluate all samples before commencing the actual experiments. Testing must confirm sample integrity before proceeding with formal analyses.

Deliverables

In the technical report, MtoZ Biolabs will provide you with detailed technical information, including:

Experimental ProceduresRelevant Spectrometric ParametersComprehensive Details on Identified Acylation SitesMass Spectrometry ImagesRaw Data

S-nitrosylation (SNO) is the covalent attachment of some nitroso (NO) groups to sulfhydryl residues (S) in proteins, forming S-nitrosothiols (SNOs). These groups are subsets of specific cysteine residues, leading to the formation of S-nitrosylated proteins. SNOs have a short half-life in the cytosol due to various reductases, such as glutathione (GSH) and thioredoxin, which act to remove the nitroso groups. Therefore, SNOs are predominantly stored in protected environments like plasma membranes, vesicles, intercellular substance, and the folds of lipophilic proteins to prevent denitrosylation. For instance, caspases involved in apoptosis are stored as SNOs within the intermembrane spaces of mitochondria. MtoZ Biolabs provides integrate S-Nitrosylation Analysis Service.

SNO process is reversible, with denitrosylation, an enzyme-catalyzed reaction, reversing the modification. SNO is selective, targeting specific cysteine residues. Improper SNO can result in protein misfolding, synaptic damage, and apoptosis. Furthermore, abnormalities in SNO signaling are associated with the development of diseases such as Alzheimer's and cardiovascular conditions.

Given the challenges in detecting S-nitrosylated cysteines due to the instability of SNOs and the presence of multiple cysteines in proteins, MtoZ Biolabs offers an advanced, sensitive analytical platform for analyzing S-nitrosylated cysteines in both eukaryotic and prokaryotic systems. We have also enhanced our detection methods to provide quicker and more sensitive analyses of these modifications.

Analysis Workflow

Protein Hydrolysis in Gel or SolutionEnrichment of S-Nitrosylated Cysteines Using Specific AntibodiesHPLC Separation Followed by ESI-TOF MS/MS AnalysisMass Spectrometry Data Analysis

Ion ChromatographyHigh-Performance Liquid Chromatography (HPLC)Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS)

Top-down mass spectrometry (TDMS) is highly effective for comprehensive analysis of protein post-translational modifications (PTMs) because it evaluates intact proteins or peptides without requiring hydrolysis. This method is particularly valuable in the analysis of biopharmaceutical proteins, such as monoclonal antibodies and recombinant proteins, where it preserves many unstable modifications that are often lost during collision-induced dissociation (CID) cleavage in shotgun approaches. MtoZ Biolabs provides integrate Top-Down PTMs Analysis Service.

Figure 1. Top-Down PTMs Analysis

Employing techniques like electron capture dissociation (ECD) and electron transfer dissociation (ETD), TDMS excels at accurately measuring the masses of whole proteins or peptides, quantifying various forms of modified proteins, creating detailed modification maps with high coverage, identifying unanticipated PTMs, and sequencing multiple modifications. Despite its relative novelty and the technical challenges it faces in sample preparation and processing throughput, top-down proteomics offers distinct benefits that render it crucial for detailed PTMs characterization.

At MtoZ Biolabs, our team of skilled proteomics scientists and technicians leverages extensive experience in top-down proteomics to deliver superior PTMs characterization services.

With ongoing advancements in proteomics mass spectrometry technology, there has been a notable increase in the precision of analytical instruments, resulting in a richer dataset. While this detailed protein data is invaluable for deeper scientific investigation, the vast volumes of data produced by high-throughput proteomic screenings introduce substantial challenges in analyzing protein sample characteristics. Due to the complexity of handling such extensive mass spectrometry data manually, it is imperative to apply advanced bioinformatics techniques for effective analysis. MtoZ Biolabs boasts a team of bioinformatics analysts who excel in the extraction of insights from proteomics data, particularly focusing on the analysis of biological pathways and networks to swiftly identify extensive protein interactions. Leveraging advancements in bioinformatics analytical methods, we have developed a comprehensive platform for proteomics data analysis. Our suite of bioinformatics solutions encompasses quality assessment of omics data, differential expression analysis, annotation and enrichment analysis through GO, KEGG, and COG, as well as protein clustering and the analysis of interaction networks and pathways at multiple levels. Furthermore, we offer tailored bioinformatics services based on client specifications and scholarly references, enabling the extraction of valuable biological insights from high-throughput experimental data. This support aids our clients in areas such as drug development, toxicity testing, and the identification of disease markers. MtoZ Biolabs provides integrate Proteomics Bioinformatic Analysis Service.

Services at MtoZ Biolabs

Proteomic Data QualityDifferential Protein Statistical AnalysisGO Functional Annotation and Enrichment AnalysisKEGG Pathway and Enrichment AnalysisCOG Functional Annotation and Enrichment AnalysisDifferentially Expressed Proteins Custer AnalysisProtein Interaction Analysis

To validate the selection of differentially expressed proteins or characteristic differentially expressed proteins, cluster analysis can be performed to group proteins based on expression trends, facilitating more intuitive proteomic data analysis. MtoZ Biolabs provides integrate Differential Proteins Clustering Analysis Service.

Services at MtoZ Biolabs

Hierarchical Cluster AnalysisK-means Cluster Analysis

The COG (Clusters of Orthologous Groups) database is an early and widely used resource for the homologous classification of gene products, based on extensive comparisons of protein sequences from various organisms. MtoZ Biolabs provides integrate COG Functional Annotation Analysis Service.

Differential protein analysis can significantly enhance the discovery of new biomarkers, improving the accuracy of biomarker identification and providing valuable insights for clinical disease analysis. MtoZ Biolabs offers precise differential protein analysis based on statistical data, identifying significant differences in protein levels under various physiological conditions and tissues. In the statistical analysis of differential expressed proteins, FC 1.3 (or 1/1.3) is used as the threshold. Proteins with FC 1.3 are considered up-regulated, while those with FC 1/1.3 are considered down-regulated. The number of differential expressed proteins is summarized in the table below. MtoZ Biolabs provides integrate Differential Protein Analysis Service.

Table 1. Statistical analysis of differential expressed proteins

The Venn diagram illustrates the shared and unique differential expressed proteins between two groups:

Figure 1. Venn Diagram of differential Expressed Proteins

Volcano Plot

The volcano plot provides a rapid visualization of the differences in protein expression levels between two sample groups and the statistical significance of these differences.

Figure 2. Volcano Plot of Differential Expressed Proteins

Note: Each point in the volcano plot represents a protein. The x-axis shows the log fold change in expression levels between the two samples, while the y-axis indicates the t-test p-value. A larger absolute value on the x-axis signifies a greater fold change in expression levels between the samples; a higher value on the y-axis denotes more significant differential expression, enhancing the reliability of identified differential expressed genes. Green dots represent down-regulated proteins, red dots represent up-regulated proteins, and black dots indicate non-differential expressed proteins.

The Gene Ontology (GO) is a database created by the Gene Ontology Consortium to provide a standardized vocabulary for gene and protein functions across species, which evolves with ongoing research. It uses a dynamic controlled vocabulary to describe the roles of genes and proteins within cells, offering a comprehensive description of gene and gene product attributes. The GO database is divided into three main categories: biological process (BP), cellular component (CC), and molecular function (MF), each describing potential molecular functions, cellular locations, and biological processes of gene products. Each node in the GO database, identified by unique names such as Cell, Fibroblast Growth Factor Receptor Binding, or Signal Transduction, and a unique identifier like GO:nnnnnnn, is annotated based on protein IDs mapped from the Uniprot database. The proteins are then functionally classified. The number of proteins associated with each GO node in BP, CC, and MF is listed, and statistical graphs of the secondary classification of expressed proteins are provided. MtoZ Biolabs provides integrate GO Functional Annotation and Enrichment Analysis Service.

Services at MtoZ Biolabs

GO Secondary Classification AnalysisGO Levels Classification AnalysistopGO Protein Enrichment Analysis

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database used for systematic analysis of metabolic pathways and functions of gene products in cells. KEGG combines gene with its expression information as a whole network. KEGG records data from genome, chemical molecule, and biochemical system, including metabolic pathways (PATHWAY), drugs (DRUG), diseases (DISEASE), gene sequences (GENES), and genomes (GENOME). MtoZ Biolabs provides integrate KEGG Pathway Annotation and Enrichment Analysis Service.

Statistics of KEGG Mapping Results for All Identified Proteins

Statistics of KEGG Annotation Results for All Identified Proteins

KEGG Pathway Annotation

In organism, different gene products coordinate to exercise biological functions. Pathway annotation analysis of differentially expressed genes helps to further understand the functions of genes. Pathway annotation diagram for differentially expressed proteins is as follows:

Figure 1. Pathway Diagram of KEGG Annotation Results

Note: Compared to the control group, enzymes marked in red are related to upregulated proteins; enzymes marked in green are related to downregulated proteins; enzymes marked in blue are related to both upregulated and downregulated proteins. The numbers inside the boxes represent the number of enzyme (EC number), and the entire pathway consists of complex biochemical reactions catalyzed by various enzymes. This pathway diagram marks enzymes related to differentially expressed genes in different colors, which focuses on the study of the differential expression of certain metabolic pathway-related proteins according to the difference among subjects and explains the root causes of phenotypic differences through the pathway.

KEGG Pathway Classification

The annotation results of differentially expressed genes in KEGG are classified according to the pathway types in KEGG, results are shown in the following figure:

Figure 2. KEGG Classification Diagram of Differentially Expressed Proteins

Note: The vertical axis is the name of the KEGG metabolic pathway, and the horizontal axis represents the number of proteins annotated to that pathway and their proportion of the total annotated proteins.

KEGG Pathway Enrichment

Analysis of whether differentially expressed proteins are over-represented in a certain pathway is termed pathway enrichment analysis for differentially expressed proteins. We use Kobas software to perform KEGG pathway enrichment analysis for differentially expressed proteins. The results of the KEGG pathway enrichment analysis for differentially expressed proteins are shown in the following figure:

Figure 3. KEGG Pathway Enrichment Statistics Diagram of Differentially Expressed Proteins

Note: Each point in the diagram represents a KEGG pathway, with the pathway name on the left axis. The horizontal axis represents the enrichment factor, a ratio that the proportion of differentially expressed proteins annotated to the pathway to the proportion of proteins in that species annotated to a pathway. The higher the enrichment factor, the more reliable the significance of enrichment of differentially expressed proteins in that pathway.

STRING is a database that records predicted and experimentally validated protein-protein interactions (PPIs) across multiple species, including direct physical interactions and indirect functional associations. By integrating the results of differential expression analysis and the interaction pairs recorded in the database, a differential expression protein interaction network is constructed. During the analysis, differentially expressed proteins are mapped to the STRING database to obtain information on their interaction relationships. As the STRING database includes experimental data, results from text mining of PubMed abstracts, and aggregated data from other databases, as well as predictions made using bioinformatics methods, we select interaction pairs with a combined score greater than 0.4 (Medium) from the search results and use appropriate bioinformatics analysis software to visualize the interaction results. The results are shown in the below. MtoZ Biolabs provides integrate Protein Interaction Network Analysis Service.

Figure 1. Evidence of Differential Expressed Protein Interactions from Different Sources (Evidence)

Figure 2. Graph of Differential Expressed Protein Interaction Strengths (Confidence)

Note: Circles (nodes) represent proteins; Different colors indicate different proteins, and the circles contain the three-dimensional structure of the proteins. Lines indicate the interactions between proteins. Thicker lines indicate stronger interaction relationships. Dark lines indicate relationships in the evidence view circle but no relationships in the actions diagram.

Figure 3: Different Action Modes between Differential Expressed Proteins (Actions)

Proteomics mass spectrometry data is fundamental to proteomics analysis. The quality of the mass spectra is closely related to the accuracy of the retrieval and analysis results. Therefore, the quality assessment of proteomics data is particularly important. To ensure the reliability of bioinformatics analysis, MtoZ Biolabs evaluates proteomic data identified from the following four aspects. MtoZ Biolabs provides integrate Proteomics Data Quality Assessment Service.

Peptide Match Error DistributionPeptide Count DistributionPeptide Length DistributionProtein Molecular Weight DistributionAnalysis of Peptide Match Error Distribution

The error distribution between the molecular weight of all matched peptides and their theoretical molecular weight is shown in the following diagram:

Analysis of Peptide Count Distribution

The distribution of peptide counts in the identified proteins is shown in the following diagram:

Note: The horizontal axis represents the count of peptides, and the vertical axis represents the number of proteins.

Analysis of Peptide Length Distribution

The distribution chart of the lengths of the identified peptides is as follows:

Note: The horizontal axis represents the length of peptides, and the vertical axis represents the number of peptides.

Analysis of Protein Molecular Weight Distribution

Note: The horizontal axis represents the molecular weight of proteins, and the vertical axis represents the number of proteins.

Two-dimensional difference gel electrophoresis (2D-DIGE) is a novel quantitative proteomics technique that evolved from traditional two-dimensional gel electrophoresis (2-DE). The principle of 2D-DIGE for separating mixed proteins is the same as traditional 2-DE. It uses differences in protein isoelectric points and molecular weights to separate protein mixtures. At the same time, the sensitive fluorescent dyes and the internal standard make it significantly better than traditional 2-DE in quantitative proteomics. The fluorescent dyes used in DIGE are Cy2, Cy3, and Cy5, which react with the lysine side chain amino groups of proteins to label the proteins without affecting their isoelectric points and molecular weights. After mixing equal amounts of the labeled proteins, two-dimensional electrophoresis is conducted. The internal standard Cy2 is used to match different gels and eliminate gel viriation, while changes in protein expression levels are reflected by fluorescence intensity of Cy3 and Cy5. As a classic method of quantitative proteomics, 2D-DIGE is widely applied and suitable for various samples. MtoZ Biolabs provides integrate 2D-DIGE Based Protein Quantitative Service.

Figure 1. 2D-DIGE Quantitative Proteomics

MtoZ Biolabs provides SDS-PAGE and 2D-DIGE services. Combining Thermo Fisher's Orbitrap Fusion Lumos mass spectrometer platform and nanoLC-MS/MS nano-liquid chromatography, We provide comprehensive proteomics identification and quantification services for researchers.

Sample Submission Requirements

Both Liquid and Solid Samples are Acceptable

Applications

Suitable for Various Samples

Service at MtoZ Biolabs

Experimental ProceduresRelevant Experimental ParametersGel and Mass Spectrometry ImagesRaw DataResults of the 2D-DIGE Quantitative Proteomics Analysis

Relative quantification of proteins is a MS-based technique that compares the relative proteins expression levels between different samples, analyzing differential protein expression under different conditions and revealing the role of proteins in biological processes. Commonly used methods include stable isotope labeling by amino acids in cell culture (SILAC), isobaric tags for relative and absolute quantification (iTRAQ), and tandem mass tags (TMT). They achieve relative quantification by enzymatic digestion, isotopic labeling, separation, and mass spectrometric analysis. MtoZ Biolabs provides integrate Relative Protein Quantitative Service, MS Based.

MtoZ Biolabs offers protein relative quantification services based on Thermo Fisher's Orbitrap Exploris 240 mass spectrometry platform combined with nanoLC-MS/MS nanoscale chromatography, using multiple relative quantification techniques such as isotopic labeling (e.g., SILAC, TMT, iTRAQ) and label-free methods (e.g., SWATH-MS, DDA). We precisely compare protein expression levels across different experimental conditions or biological samples, identify protein-level changes, and help clients rapidly and accurately assess differences in protein expression levels to reveal the molecular mechanisms of biological processes, disease onset, and drug therapy.

Analysis Workflow

Sample Preparation

Proteins extraction from different biological samples using suitable methods according to project requirements, followed by purification, concentration, and quality assessment to ensure the sample meets experimental requirements.

Protein Digestion

Protein digestion by various enzymes into peptide for subsequent mass spectrometry analysis.

Isotopic Labeling

Peptide labeling by isotopic labeling methods such as SILAC, iTRAQ, or TMT.

Peptide Separation

Peptide separation by HPLC (e.g., RP-HPLC).

Mass Spectrometric Analysis

Analysis and detection of peptides by high-resolution mass spectrometry to obtain data on mass, m/z and other information.

Data Analysis

Analysis of mass spectrometry data by specific bioinformatics software to identify and relatively quantify proteins to find significantly different proteins by comparing differential protein expression under different conditions.

Service Advantages

High-Throughput Data Acquisition

Advanced Orbitrap Exploris 240 mass spectrometer with high-sensitivity, high-resolution protein detection to quickly acquire large amounts of protein data.

Accurate Quantitative Analysis

Efficient data processing workflows and software for accurate and reliable protein quantification.

High Sensitivity

Ability to detect low-abundance proteins with high sensitivity.

Broad Applicability

Suit for a wide range of biological samples, including cells, tissues, and body fluids to study various biological processes.

Customized Analytical Solutions

One-stop services including experimental design, sample processing and data analysis according to project requirements.

Applications

Gene Expression Regulation Studies

Compare protein expression differences under different conditions to study the effects of post-transcriptional regulation and post-translational modifications on gene expression.

Signal Transduction Pathway Studies

Use quantitative analysis of differential protein expression of signal molecules to reveal activation and inhibition mechanisms of signaling pathways.

Comparative Proteomics Studies

Compare protein expression differences among species or subtypes to explore genetic variation, evolutionary relationships, and functional differences in species.

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Data-independent acquisition (DIA) is a non-dependent data scanning mode, a holographic mass spectrometry data acquisition mode based on the electrostatic field orbitrap. After primary mass spectrometric detection, all ionized compounds of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion. The fragment ions of all precursor ions are collected, and quickly scaned within precursor isolation window to perform protein qualitative and quantitative analysis. Compared to data-dependent acquisition mode (DDA), DIA has better accuracy and reproducibility. The SWATH technique is a DIA technique that integrates the high-throughput detection of shotgun proteomics with the precise quantitative analysis of parallel reaction monitoring (PRM). It can quantify almost all detectable molecules in complex samples. MtoZ Biolabs provides integrate DIA based Protein Quantitative Service.

MtoZ Biolabs offers DIA quantitative proteomics service, including the AB SCIEX Triple-TOF 5600 plus high-resolution mass spectrometry system, which features fast scanning speed and quantitative sensitivity of tandem quadrupole mass spectrometry systems and integrates high resolution, accurate mass stability, high sensitivity, and high-speed scanning of the mass spectrometry system. You only need to send us your samples, and we will take care of all subsequent project matters, including protein extraction, protein digestion, peptide separation, mass spectrometric analysis, raw mass spectrometric data analysis, and bioinformatics analysis.

Applications

It can be applied to various bioscience research in agriculture, forestry, environment, food, and medicine to build biological sample database and discover biomarkers.

Service at MtoZ Biolabs

Experimental ProceduresRelevant Mass Spectrometric ParametersMass Spectrometric ImagesRaw DataProtein Differential AnalysisBioinformatics Analysis

In scientific research, there are two main types of analysis: qualitative and quantitative analysis. Between qualitative and quantitative analysis, there is a semi-quantitative analysis, which yields approximate measurement value rather than precise one. Semi-quantitative analysis is often used when direct measurement of results is challenging while the conclusions drawn from inference are insufficient, especially when quantitative data are likely to fluctuate periodically. MtoZ Biolabs provides integrate Semi Quantitative Proteomic Analysis Service.

Services at MtoZ Biolabs

GO Function Annotation and Enrichment AnalysisCOG Function Annotation and Enrichment AnalysisDifferential Protein Expression Clustering AnalysisProtein-protein Interaction Network AnalysisDifferential Protein Statistics Analysis

Proteomics is a scientific field that studies the composition, structure, function, and interactions of all proteins in an organism. Its goal is to establish a comprehensive protein information library and understand their roles in life. However, the proteins whose biological functions have been thoroughly studied are still few, and some protein-coding genes still lack relevant annotations. Nonsynonymous single nucleotide polymorphisms, a large variety of proteins produced by alternative splicing and post-translational modifications of proteins, make gene annotation more difficult. The emergence of high-throughput gene knockout technology provides a powerful tool for the detection of large-scale protein and their forms. High-throughput gene knockout technology can be used to silence or knockout specific genes to observe changes in the proteome. Combined with high-resolution mass spectrometry, it can be used to analyze protein composition, modifications, and relative abundance. MtoZ Biolabs provides integrate High-Throughout Proteomics Analysis Service for Gene Knockout.

The combination of high-throughput gene knockout technology and proteomics provides a new perspective for biological research. By combining these two technologies, researchers can study the impact of specific gene knockouts on the proteome, and identify proteins associated with the knocked-out genes, which help better understand the interactions between genes and proteins, and reveal protein regulatory networks. For example, researchers can determine how the knockout of a specific gene affects protein expression in cancer cells to discover new cancer treatment methods. Furthermore, this combination can also be used to study the mechanisms of various diseases such as neurodegenerative disease, immune disease, and metabolic disorder.

MtoZ Biolabs, based on the high-resolution proteomics analysis platform combined with high-throughput gene knockout technology, can provide you with a comprehensive solution from gene knockout to proteomics analysis. Our advanced CRISPR/Cas9 system can achieve single/multiple gene knockouts of human/mouse cell lines, primary cells, immune cells, and iPS cells, frameshift mutations, and large sequence deletions. When KO cells obtained, they are cultured and the proteins expressed by them are extracted. Using a high-resolution mass spectrometry platform for their proteomics analysis, the specific role of the knocked-out gene at the protein level is elucidated, revealing the mechanism how genes regulate proteins. MtoZ Biolabs aims to provide you with the highest quality scientific research service. We look forward to cooperating with you. Welcome to contact to learn more about our service.

Service Advantages

High Knockout Efficiency

Optimized CRISPR/Cas9 system with over 80% target knockout efficiency at 70%; after gene knockout, we use Sanger sequencing and in-depth proteomics technology to doubly verify the knockout efficiency to ensure the accuracy of the data.

Comprehensive Proteomics Analysis Platform

Our proteomics analysis platform is equipped with comprehensive sample pre-treatment instruments, high-specificity protein modification enrichment platform, ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry, and protein N-terminal sequence analyzer, which can achieve efficient protein extraction at the omics level, high-efficiency enrichment of specific modified peptides, and protein identification, relative quantification (3D & 4D), and absolute.

Proteomics analysis includes analyzing the structure and function of proteins, post-translational modifications (PTMs), protein localization, protein expression, and the interactions among proteins, etc. Based on different analytical content, different proteomics analysis techniques and strategies can be adopted. MtoZ Biolabs provides integrate Proteomics Analysis Strategy Service.

Mass spectrometry (MS) is one of the most commonly used techniques in proteomics analysis. Currently, proteomics analysis strategies based on MS mainly include bottom-up proteomics and top-down proteomics. In bottom-up proteomics, proteins need to be digested into peptides before mass spectrometric analysis, and this strategy is adopted by common label-free and labeling quantitative proteomics techniques. In top-down proteomics, protein are not digested but are directly analyzed, which can preserve most of the features of proteins with unstable structures that are mostly destroyed in the bottom-up strategy, and also reduces the time consumption of digestion. Researchers can choose the appropriate strategy for proteomics analysis according to different research needs.

MtoZ Biolabs provides various proteomics analysis services using the Thermo Fisher Orbitrap Fusion Lumos mass spectrometry platform combined with nanoLC-MS/MS nanoscale chromatography.

Services at MtoZ Biolabs

Top-down ProteomicsDIA-PRM ProteomicsPCT-DIA Proteomics

Data-independent acquisition (DIA) is a holographic mass spectrometry data acquisition mode based on the electrostatic field Orbitrap and is a data-independent scanning mode. Compared to data-dependent acquisition mode (DDA), DIA technology divides the entire scanning range of mass spectrometry into several windows, selecting, fragmenting, and detecting all ions within each window, providing better accuracy and repeatability. PRM (parallel reaction monitoring) is an ion monitoring technology based on high-resolution and high-precision mass spectrometry, which is currently the mainstream method for targeted proteomics data acquisition. By selectively detecting specific or target peptides (such as post-translational modification peptides), it enables targeted relative or absolute quantification of target proteins/modification peptides. Combining DIA and PRM for proteomics research can achieve detection of large or complex samples and precise quantification of target proteins, especially improving the detection rate of low-abundance target proteins. MtoZ Biolabs provides integrate DIA-PRM Proteomics Service.

MtoZ Biolabs uses Thermo's latest Obitrap Fusion Lumos mass spectrometer combined with Nano-LC nanoliter chromatography technology to provide a DIA+PRM proteomics analysis service. You only need to send us your samples, and we will handle all subsequent project matters, including protein extraction, protease digestion, peptide separation, mass spectrometric analysis, mass spectrometric raw data analysis, and bioinformatics analysis.

Applications

It can be applied to the fields of agriculture and forestry, environment, food, and medicine to construct biological sample information databases and discover biomarkers in various biological science studies.

Deliverables

Experimental ProceduresMass Spectrometry ParametersMass Spectrometry ImagesRaw DataProtein Differential Level AnalysisBioinformatics Analysis

Pressure cycling technology (PCT) is an efficient biological sample preparation technology and a patented technology developed by Pressure BioSciences Inc (PBI), USA. It uses pressure cycling between atmospheric pressure and ultra-high (liquid) pressure (35, 000 PSI or higher), repeatedly breaking cells and enabling the extraction of important biomolecules such as proteins from various samples (cells and tissues from humans, animals, plants, and microorganisms). Data-independent acquisition (DIA) is a holographic mass spectrometry data acquisition mode based on the electrostatic field Orbitrap and is a data-independent scanning mode. Compared to data-dependent acquisition mode (DDA), DIA technology divides the entire scanning range of mass spectrometry into several windows, selecting, fragmenting, and detecting all ions within each window, providing better accuracy and repeatability. The combination of PCT and DIA technologies allows the study of the proteome of paraffin-embedded or formalin-fixed tissue samples and trace samples. MtoZ Biolabs provides integrate PCT-DIA Proteomics Service.

MtoZ Biolabs, using Thermo's latest Obitrap Fusion Lumos mass spectrometer combined with Nano-LC nanoliter chromatography technology, offers a PCT+PRM proteomics analysis service. You only need to send us your samples, and we will take care of all subsequent project procedures, including protein extraction, protease digestion, peptide separation, mass spectrometry analysis, raw data analysis, and bioinformatics analysis.

Analysis Workflow

Guo, T. et al. iScience. 2019.

Figure 1. PCT+DIA Proteomics

Deliverables

Experimental ProceduresRelevant Mass Spectrometry ParametersMass Spectrometry ImagesRaw DataProtein Differential Level AnalysisBioinformatics Analysis

Plant Proteomics is a branch of proteomics aimed at studying the composition, structure, function, interactions, and regulatory mechanisms of plant proteins. Its research methods are similar to those in proteomics with core techniques used in protein separation, purification, identification, functional annotation, interaction studies, and expression regulation studies. Research in plant proteomics can not only provide a material basis for understanding the law of plant growth, development, and stress adaptation but also offer theoretical foundation and solution for improving crop resistance and quality. By comparing the proteome of plants growing in different conditions, different plant varieties, and individuals under normal and stressed conditions, we can identify specific protein that can serve as targets for genetic improvement and biotechnological strategies or provide molecular markers for the impact of environmental changes on plant growth. MtoZ Biolabs provides integrate Plant Proteomics Service.

Services at MtoZ Biolabs

Protein Identification and Functional Annotation

Using high-resolution mass spectrometry (Thermo Fisher's Q Exactive and Orbitrap mass spectrometers) combined with bioinformatics databases and software, we identify detected proteins and provide detailed functional annotation.

Quantitative Proteomics Analysis

We offer labeled (iTRAQ, TMT, SILAC) and label-free methods for quantitative protein analysis.

Protein-Protein Interaction Studies

Techniques like immunoprecipitation (IP), Co-immunoprecipitation (Co-IP), and affinity purification mass spectrometry (AP-MS) are used to study the interactions between proteins of interest and other proteins. Subsequently, LC-MS/MS is used to identify proteins/protein mixtures in purified samples such as IP, Co-IP, and GST fusion protein pull-down samples.

Protein Post-Translational Modifications (PTMs) Analysis

We offer identification and quantification of PTMs like phosphorylation, glycosylation, ubiquitination, acetylation, methylation, disulfide bonds, nitrosylation, and modification sites.

Differential Protein Expression Analysis

By comparing proteomic data of plants under different treatment conditions, we perform statistical analysis of differential protein expression (Venn diagrams, volcano plots) and clustering analysis (hierarchical clustering analysis, K-means clustering analysis).

Applications

Gene Research

Analyzing differential expression of plant proteins provides information in gene function prediction, gene regulatory network research, and plant physiological ecology.

Agricultural Improvement

Studying protein components and metabolic pathways of plant products can offer references for agricultural biotechnology.

Ecological Research

Understanding the biological mechanisms behind plant adaptive changes can aid ecological protection and biodiversity research.

Plant Disease Diagnosis

Researching the molecular mechanisms of diseases can provide important information for disease diagnosis and prevention.

Sample Submission Requirements

Fresh Tissues: Leaves, roots, stems, flowers, seeds, etc.; at least 100 mgDried Tissues: Plant tissues processed by freeze-drying or drying; at least 50 mgCells: Plant cell suspension or cell lysate; at least 1x107 cellsProtein Extracts: Protein samples extracted, at least 100 g with their concentration not less than 1 g/L

Deliverables

Experimental ProceduresRelevant Mass Spectrometry ParametersDetailed Information on Plant Proteomics AnalysisMass Spectrometry ImagesRaw Data

Cellular proteomics is a scientific discipline that explores the expression, modification, interaction, and function of all proteins within cells. As a significant branch of proteomics, the development of cellular proteomics is closely linked to the progress of proteomics itself. In 1995, the term "proteomics" was introduced, marking the official start of proteomics research. With advancements in mass spectrometry technology, studies on intracellular proteins became increasingly sophisticated. In the early 21st century, cellular proteomics emerged as a subfield of proteomics, gaining widespread attention. Since then, new technologies and methods have continuously driven progress in this field, providing critical insights into cell biology, disease mechanisms, and drug development. MtoZ Biolabs provides integrate Cellular Proteomics Service.

Currently, the primary technical methods in cellular proteomics include: 2D gel electrophoresis and liquid chromatography to separate proteomes into different subgroups for easy identification and quantification; mass spectrometry analysis to identifies protein sequences and modification states using high-resolution tandem mass spectrometry; immunoprecipitation and affinity purification to capture the target proteins and highly purify the proteins using specific antibodies or ligands; and bioinformatics analysis to reveal the biological significance of the proteins by integrating, mining, and visualizing the histological data.

Analysis Workflow

Protein Extraction

Disrupt cells and remove non-protein components such as lipids, nucleic acids, and small metabolites.

Protein Separation and Purification

Use 2D gel electrophoresis and liquid chromatography to separate and purify protein samples

Protein Identification

Apply high-resolution tandem mass spectrometry (MALDI-TOF MS, ESI-MS/MS, etc.) to analyze the purified proteins, identifying their sequence and structural information.

Protein Quantification

Conduct quantitative analysis using isotope labeling methods (e.g., iTRAQ, TMT, SILAC) and label-free methods (e.g., Label Free, SWATH-MS) to compare protein expression differences under different conditions.

Data Processing and Analysis

Process, analyze, and interpret mass spectrometry data using bioinformatics methods, including protein identification, quantitative analysis, protein function annotation, interaction network analysis, and pathway analysis.

Service Advantages

High Throughput

Leveraging HPLC and mass spectrometry, a large number of proteins can be identified and quantified in a short period of time.

High Efficiency

Bioinformatics tools can mine, integrate, and visualize large datasets.

Diversity

Suitable for various organisms and cell types, cellular proteomics analysis can be used to study protein changes under different environments, disease states, or genetic mutations.

Systematic

By comprehensively revealing the expression, modification, and interaction of all proteins within cells, it provides systematic and holistic information for biological research.

Sample Submission Requirements

In the technical report, MtoZ Biolabs will provide you a detailed technical information, including:

Experimental ProceduresRelevant Mass Spectrometry ParametersCellular Proteomics Analysis DetailsMass Spectrometry ImagesRaw Data

Cell surface proteins form a unique class of proteins, playing critical roles in managing cell function and facilitating communication between the cell and its environment by transporting metabolites, ions, and other solutes. MtoZ Biolabs provides integrate Cell Surface Proteomics Service.

Cell surface proteins vary across different cell types and can even change within a specific cell type under normal or diseased conditions. Consequently, cell surface proteins have numerous significant applications, such as distinguishing cell phenotypes and disease states and aiding research and development for prognosis and therapeutic targets. The cell surface contains key biomarkers and potential drug targets for various diseases. Approximately 70% of current biopharmaceuticals in development target cell surface proteins, underscoring the importance of studying surface proteins and their potential role in developing novel cancer therapies.

MtoZ Biolabs provides specialized and comprehensive cell surface proteomics services for identifying and quantifying the cell surface proteome, encompassing the entire mass spectrometry analysis workflow, from cell surface protein extraction to protein identification and quantification.

Leveraging biotin affinity purification technology, MtoZ Biolabs has optimized protocols for cell surface protein purification and enrichment, enabling high-quality extraction and enrichment of cell surface proteins for subsequent proteomic analysis. The company uses the Orbitrap Fusion Lumos mass spectrometer, the latest high-resolution, high-sensitivity instrument from Thermo, in combination with nanoLC chromatography for comprehensive cell surface proteomics analysis. With robust bioinformatics capabilities and extensive experience in bioinformatics analysis, our technicians can proficiently utilize various bioinformatics analysis tools to conduct in-depth data analysis and mining, allowing for effective screening of potential biomarkers.

Exosomes are one of the common extracellular vesicles (EVs) with diameters ranging from 30 to 150 nm. They primarily originate from the invagination of lysosomal particles into multivesicular bodies, which are released into the extracellular matrix, such as tissues and various biological fluids including serum/plasma, cerebrospinal fluid, and urine (in vivo), after the outer membrane of the multivesicular body fuses with the cell membrane. Additionally, exosomes can also exist in vitro under certain conditions in culture media. EVs play an important role in various physiological processes, and compared to general EVs, the function of exosomes in the field of clinical biomarkers is still unclear. With the development of exosome separation technologies, interest in this field is growing, and it is anticipated that more detailed studies on the function and applications of exosomes in disease pathologies will emerge. MtoZ Biolabs provides integrate Exosome Proteomics Service.

Exosomes primarily contain a complex mixture of proteins, lipids, RNA, etc. The content and function of exosomes from different biological fluids vary, and compared to other contents, proteins play a crucial role in biological functions. Therefore, proteomic analysis of exosomes from different biological samples is significant for the discovery of biomarkers and clinical diagnosis.

MtoZ Biolabs provides professional and comprehensive exosomal proteomics analysis services, capable of identifying and quantifying proteins in exosomes. By integrating bioinformatics techniques for the analysis of proteomic data, the detection of biomarkers can be achieved.

Figure 1. Saliva and Serum Exosome Proteomics Workflow (Y. Sun et al., 2017)

Service Advantages

One-stop Exosome Proteomics Analysis

We can complete the entire process including exosome separation to protein identification and quantification. It is possible to separate exosomes from various types of samples, including plasma/serum, cerebrospinal fluid, saliva, snot, urine, bile, and cell culture media.

Advanced Facilities and Optimized Operation Procedures

MtoZ Biolabs uses the currently highest resolution and sensitivity mass spectrometer, the newly introduced Obitrap Fusion Lumos by Thermo company, combined with nanoLC chromatography for exosomal proteomics analysis. MtoZ Biolabs has extensive experience in the field of exosome proteomics analysis and can provide customized services.

Biomarker Detection through Bioinformatics Analysis

Our professional bioinformatics analysts are proficient in using various bioinformatics analysis tools, providing in-depth analysis and data mining.

For mass spectrometry-based proteomic analysis, animal samples typically include fresh tissues, blood, urine, and cells. Paraffin-embedded (FFPE) samples, especially those used clinically, offer the advantages of well-documented medical histories, accurate diagnoses, and comprehensive clinical data. They can be stably stored at room temperature for extended periods, making them highly valuable for disease research. Therefore, proteomic research on FFPE samples is of great importance in understanding disease mechanisms, identifying biomarkers, and studying rare diseases. MtoZ Biolabs provides integrate Paraffin Embedded Sample Proteomics Service.

MtoZ Biolabs uses Thermo Fisher's Orbitrap Fusion Lumos mass spectrometry platform combined with nanoLC chromatography to provide comprehensive technical solutions for FFPE sample proteomic analysis. Simply communicate your research objectives and send us your samples, and we'll handle the rest, including protein extraction, protease digestion, peptide separation, mass spectrometry analysis, raw mass spectrometry data processing, and bioinformatics analysis.

Analysis Workflow

Deliverables

In the technical report, MtoZ Biolabs will provide you with a detailed technical information, including:

Experimental ProceduresRelevant Mass Spectrometry ParametersMass Spectrometry ImagesRaw DataBioinformatics Analysis