Proteome and PTM Profiling

Service Description

Proteomics and metabolomics data are increasingly combined with genomics information in multi-omics studies to enhance basic research and drug development projects. BGI is a pioneer in the field of trans-omics and offers advanced proteomics and bioinformatics solutions to support our client’s research1,2.

Recent advances in mass spectrometry have provided powerful tools for the analysis of proteins from a variety of organisms and cell types. BGI applies state-of-the-art MS-based techniques for protein identification, protein characterization, relative and absolute quantitation, as well as for the study of post-translational modifications (PTMs) and protein-protein interactions.


Project Workflow

Proteome Profiling

Proteome Profiling is a cost effective, high value solution for monitoring hundreds-to-thousands of proteins simultaneously. Our UHPLC-UV sample fractionation services are highly recommended for complex sample types to maximize protein sequence coverage and detection dynamic range3.

We perform sample digestion using sequencing-grade trypsin or alternative proteolytic method. Trypsin-digested peptide samples are analyzed using nano-flow LC-MS/MS. Spectral counting method provides approximate protein relative abundances4.

Sample preparation

LC-UV Fractionation

LC-MS/MS analysis

Data analysis and bioinformatics


PTM Profiling

Our PTM Profiling service utilizes multiple protease digests run independently to provide high sequence coverage of detected proteins which is critical for confident PTM site identifications5.

Sample preparation

LC-UV Fractionation

LC-MS/MS analysis

Orthogonal LC-MS/MS analyses

Data analysis and bioinformatics


Phospho Enrichment Profiling

Our Phospho Enrichment Profiling service can be customized to meet the needs of your drug discovery program.

Phosphorylated peptides are enriched using titanium dioxide. For deep phopho-proteome analysis off-line fractionation is highly recommended6. We provide a full data report detailing detected protein IDs, peptide-localized PTM assignments, and PSM counts.

Sample preparation

Phospho enrichment

LC-UV Fractionation

LC-MS/MS analysis

Data analysis and bioinformatics




[1]. Xun Z, Shangbo X et al. Tissue-specific Proteogenomics Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline. Mol Cell Proteomics. 2016; 15(6): 1791-1807. doi: 10.1074/mcp.M115.050989.


[2]. Zhen C, Bo W et al. Quantitative proteomics reveals the temperature-dependent proteins encoded by a series of cluster genes in thermoanaerobacter tengcongensis. Mol Cell Proteomics. 2013; 12(8): 2266-2277. doi: 10.1074/mcp.M112.025817.


[3]. Chandramouli K, Qian PY. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Hum Genomics Proteomics. 2009 Dec 8;2009. pii: 239204. doi: 10.4061/2009/239204.


[4]. Wong, J. W. H., & Cagney, G. (2009). An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry. Proteome Bioinformatics, 273–283.doi:10.1007/978-1-60761-444-9_18.


[5]. Giansanti P, Tsiatsiani L, Low TY, Heck AJ. Six alternative proteases for mass spectrometry-based proteomics beyond trypsin. Nat Protoc. 2016 May;11(5):993-1006. doi: 10.1038/nprot.2016.057.


[6]. Salter AI, Ivey RG, Kennedy JJ, Voillet V, Rajan A, Alderman EJ, Voytovich UJ, Lin C, Sommermeyer D, Liu L, Whiteaker JR, Gottardo R, Paulovich AG, Riddell SR. Phosphoproteomic analysis of chimeric antigen receptor signaling reveals kinetic and quantitative differences that affect cell function. Sci Signal. 2018 Aug 21;11(544). pii: eaat6753. doi: 10.1126/scisignal.aat6753.

How to Order

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Mass Spectrometry Service Specification

Proteome and PTM Profiling services are performed using nano-flow liquid chromatography and high resolution Orbitrap mass spectrometry.

  • Sample Preparation and Services

    Sample Preparation and Services

    • Digestion performed using sequencing-grade trypsin
    • Off-line sample fractionation using UHPLC-UV technology
    • Each fraction analyzed using 180 min nano-flow LC-MS/MS using a Q Exactive HF-X Orbitrap mass spectrometer
    • Peptide Spectral Match (PSM) data utilized for constructing proteomic profile
  • Mass Spec Services Quality Standard

    Mass Spec Services Quality Standard

    • Summary including all methods and data analysis
    • Reports provided in Excel or PDF format, RAW files available upon request
  • Turn Around Time

    Turn Around Time

    • Typical 20 working days from sample QC acceptance to data report delivery

Sample Requirements

We accept protein samples in a variety of formats. For maximum proteome coverage complex samples can be extensively fractionated off-line using our UHPLC-UV platform.

Sample type Amount and Concentration Minimum sample volume
Protein sample in liquid solution or in gel band/spot Recommended 100 µg for each enzyme; 2 µg/µL 100 µL for each enzyme
Minimum Required 10 µg for each enzyme; 1 µg/µL 10 µL for each enzyme

Data Analysis

Advanced Bioinformatics

  • Data analysis and validation performed with SEQUEST or Mascot

  • GO (Gene ontology) category analysis

  • COG (Cluster of Orthologous Groups of proteins) category analysis

  • Pathway analysis

  • DEPs (differentially expressed proteins) cluster analysis

  • DEPs GO enrichment analysis

  • DEPs pathway enrichment analysis

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