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Modified Proteome Analysis

Modified Proteome Analysis Online Inquiry

A global biological information analysis service provider, CD Genomics provides services for modified protein data analysis to help you understand the post-translational modification of proteins by different functional groups. We use bioinformatics to analyze protein spectrum data modified by different functional groups and provide perfect solutions for different types of modified mass spectrometry data analysis. To make your work easier, once you provide us the data to be analyzed, we will complete the rest and provide you the most easy-to-interpret analysis result report.

Introduction to Modified Proteome Analysis

A specific position in the amino acid sequence of a protein can be covalently bound to a chemical group or a small molecular weight protein to cause protein post-translational modifications (PTMs), potentially occurring on the side chain or C-terminal and N-terminal of amino acids. Protein functions can be extended by modifying the existing 20 amino acid functional groups or introducing new groups (such as phosphate groups, acetyl groups, etc.). The proteins expressed by most eukaryotes need to undergo a series of post-translational processing and modification to form the final complex functional executive body. Therefore, protein PTMs have become an important direction of proteomics research.

The common protein modifications in organisms include phosphorylation, glycosylation and acetylation, and ubiquitination, which regulate the active state, localization, folding, function and interaction of proteins. These modifications are important in many cellular processes, such as signal transduction, cell differentiation, cellular immunity, transcriptional regulation and so on. With the development of biotechnology, the combination of affinity enrichment, multidimensional separation and other technologies with biological mass spectrometry provides an opportunity for the development of PTM proteomics, which has resulted in a large amount of PTM proteomics data. Using bioinformatics, we can qualitatively and quantitatively analyze the protein modification status at the protein modification level to obtain modification differences under different treatments or different physiological and pathological conditions, laying a solid data foundation for subsequent protein research.

Schematic diagram of identification of protein post-translational modification (acetylation).Fig 1.Schematic diagram of identification of protein post-translational modification (acetylation). (Kori Y, et al 2017)

  • Data analysis
  • Phosphorylation
  • Acetylation
  • Glycosylation
  • Ubiquitination

What we can do

CD Genomics provides identification and analysis of protein PTMs by different functional groups such as phosphorylation, glycosylation, ubiquitination, acetylation, etc.

Advantages of CD Genomics

Experienced protein research team

Rich experience in bioinformatics data analysis

Comprehensive analysis content

Multi-omics joint customized analysis

Intuitive and beautiful charts

Thoughtful after-sales service

CD Genomics Data Analysis Pipeline

CD Genomics modified proteome data analysis pipeline - CD Genomics.

Bioinformatics Analysis Content

When a protein undergoes post-translational modification, its molecular mass will change accordingly. Mass spectrometry can accurately determine the molecular mass of a protein or peptide. By means of bioinformatic analysis, PTMs in samples can be relatively quantified, and differentially modified sites and differentially modified proteins can be screened. The following analysis is applicable to the identification and analysis of protein PTMs modified by different functional groups.

Data quality assessment Statistical analysis of data
Protein sequence search
Qualitative protein analysis Protein identification results
Post-translational modification site
Protein coverage distribution
Unique peptide number distribution
Modification site analysis Modified functional group category statistics
Distribution of modification sites
Protein quantitative analysis Protein quantification results
Repeatability analysis
Modified protein quantitative analysis
Protein function annotation GO Enrichment analysis
KEGG Enrichment analysis
COG Enrichment analysis
Domain Enrichment analysis
Protein difference analysis Odds ratio analysis
Volcano map analysis
Cluster analysis
Analysis of GO Enrichment of Differential Proteins
COG/KOG analysis of differential proteins
Pathway Enrichment Analysis of Differential Proteins
Protein interaction networks analysis
Association analysis with quantitative proteome Proteome and modified proteome expression regulation analysis
Correlation analysis of expression level of proteome and modified proteome
GO function enrichment correlation analysis
KEGG signaling pathway enrichment analysis

For other analysis needs on modified proteome data analysis, we will provide the right biological information analysis content accordingly. For analysis content, price, cycle, or other questions, please click online inquiry.

Turnaround Time

Modified proteome data analysis turnaround time - CD Genomics.

About one to two weeks, it's depends on the type of data (different types of protein modifications) and the specific scale of the project (number of samples). For more information, please contact us.

CD Genomics provides general analysis and customized analysis of modified proteome data analysis for different types of protein modification mass spectrometry data. In addition to phosphorylation, glycosylation, ubiquitination, acetylation data, if you have methylation, disulfide bond, nitrosation, succinylation, propionylation, multipathway phosphorylation modified protein post-translational modification MS data, please contact our technical support, we will provide you with the most suitable analysis based on your data. If you are interested in our services, please feel free to get in touch for more detailed information.

Reference

  1. Kori Y, et al. Proteome-wide acetylation dynamics in human cells[J]. Scientific Reports, 2017, 7(1):10296.

Importance of phosphorylation

Protein phosphorylation is a very important and widely present post-translational modification regulation method in prokaryotes and eukaryotes. It is involved in cell proliferation, development, differentiation, apoptosis, cytoskeleton regulation, neural activity, muscle contraction, metabolism, and tumor occurrence and so on. It plays a biological regulatory role in many biological cell functions. The study of phosphorylated proteome can help analyze the complex physiological and pathological processes of organisms.

Through biological information analysis of phosphorylation data, such as using Skyline20, Comet21, DIA-Umpire24 and other biological analysis software, in addition to relative quantification of post-translational phosphorylation in the sample, screening of differential phosphorylation sites and differentially expressed phosphorylated proteins, unknown new phosphorylation sites and phosphorylated proteins can also be discovered.

Phosphoproteome Oscillations inthe Mouse Livers.Fig 1. Phosphoproteome Oscillations inthe Mouse Livers. (Maria S. et al. 2017)

Application Field

Protein phosphorylation data analysis can be applied to the following fields, but not limited to the following fields

Research on the mechanism of disease occurrence and development

Disease marker screening

Drug target research

Health research

Reference

  1. Maria S. et al.,Phosphorylation Is a Central Mechanism for Circadian Control of Metabolism and Physiology [J], Cell Metabolism, 2017. 25, 1–10.

Importance of Acetylation

Acetylation modification is an evolutionarily conserved reversible post-translational modification (PTM), which exists in both prokaryotes and eukaryotes. Acetylation involves key cellular processes related to physiology and disease, such as the impact on gene transcription, DNA damage repair, cell division cycle, signal transduction, protein folding, autophagy and metabolism. At the same time, acetylation modification affects protein functions through a variety of mechanisms, including regulation of protein stability, enzyme activity, subcellular localization, crosstalk with other post-translational modifications, and regulation of protein-protein and protein-DNA interactions. The study of acetylated proteome can help analyze the complex and diverse physiological and pathological processes of life.

Through biological information analysis of phosphorylation data, such as using MaxQuant and other biological analysis software, in addition to relative quantification of post-translational acetylation in the sample, screening of differential acetylation sites and differentially expressed acetylation proteins, unknown new acetylation sites and acetylation proteins can also be discovered.

Research process of lysine acetylation of Trichoderma rubrum.Fig 1. Research process of lysine acetylation of Trichoderma rubrum. (Xu X, et al. 2018)

Application Field

Protein acetylation research can be used for basic research in the following areas.

Research on molecular mechanisms such as cell differentiation and cellular immunity

Mechanism of disease occurrence and development

Medication mechanism

Discovery of therapeutic targets

Reference

  1. Xu X, et al. The first whole-cell proteome- and lysine-acetylome-based comparison between Trichophyton rubrum conidial and mycelial stages[J]. Journal of Proteome Research, 2018 :acs. jproteome. 7b00793.

Importance of Glycosylation

Glycosylation is an important post-translational modification of proteins. It plays an extremely important role in the structure and function of proteins. Its most important function is to properly fold peptides synthesized in the endoplasmic reticulum. According to the different connection modes of sugar chains and peptide chains, protein glycosylation can be divided into N-glycosylation and O-glycosylation. Glycosylation regulates the location, function, activity, lifespan and diversity of proteins in tissues and cells, and participates in various important life activities including cell recognition, differentiation, development, signal transduction, and immune response.

Use GlycoMod and other bioinformatics analysis software to analyze protein glycosylation data, and perform qualitative and quantitative analysis of protein glycosylation modification status to obtain protein glycosylation modification differences under different processing or different physiological and pathological conditions, which will lay a foundation for subsequent research data basis. Studies have shown that various diseases, such as tumors, neurodegenerative diseases, cardiovascular diseases, metabolic diseases, immune diseases and infectious diseases, are accompanied by abnormal protein glycosylation.

MS/MS spectra of the major glycoforms of glycopeptides covering six N-glycosylation sites.Fig 1. MS/MS spectra of the major glycoforms of glycopeptides covering six N-glycosylation sites.
(Yagi H , et al. 2018)

Application Field

Protein glycosylation research can be used for basic research in the following areas.

Research on the mechanism of disease occurrence and development

Disease marker screening

Drug target research

Health research

Reference

  1. Yagi H , et al. Site-specific N-glycosylation analysis of soluble Fcγ receptor IIIb in human serum[J]. Scientific Reports, 2018, 8(1):2719.

Importance of Ubiquitination

Ubiquitination modification is an important post-translational modification, which plays a very important role in protein localization, metabolism, function regulation and degradation. At the same time, it also participates in cell cycle, proliferation, apoptosis, differentiation, and metastasis, gene expression, transcription regulation, signal transmission, damage repair, inflammation and immunity and other life activities regulation. Therefore, ubiquitination modification has almost participated in all life activities of eukaryotes.

Use GlycoMod and other bioinformatics analysis software to analyze protein abiquitination data, and perform qualitative and quantitative analysis of protein abiquitination modification status to obtain protein abiquitination modification differences under different processing or different physiological and pathological conditions, which will lay a foundation for subsequent research data basis. Studies have shown that ubiquitination is closely related to the onset of tumors, neurodegenerative diseases, muscular dystrophy, immune diseases, cardiovascular diseases and metabolic syndrome. In addition, the study of ubiquitination modification has great potential application value in improving plants' response to stress environments.

Application of protein ubiquitination modification analysis in the study of rice resistance mechanismFig 1. Application of protein ubiquitination modification analysis in the study of rice resistance mechanism. (Li X M , et al. 2015)

Application Field

Protein ubiquitination research can be used for basic research in the following areas, but not limited to the following research areas.

Disease research and treatment

Medication mechanism

Research on Plant Resistance

Reference

  1. Li X M , et al. Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice[J]. Nature Genetics, 2015, 47(7):827-33.
* For Research Use Only. Not for use in diagnostic procedures.
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