Label-free DIA Quantitation

Service Description

BGI participates in quantitative performance assessment as well as standardization and harmonization of Multi-National DIA proteomics analysis supporting precision medicine studies. We have developed innovative solutions for optimizing the process of accurately quantifying proteins in complex biological matrices and other complex mixtures.


Label-Free DIA Quantitative Proteomics

Data-Independent Acquisition (DIA) is a label-free quantitative technique which provides highly consistent quantitation and broad proteome coverage1. We create a customized spectral library with your specific sample and then analyze individual samples using nano-flow LC-MS/MS with DIA scanning and quantitation2.

Label-Free DIA Quantitative Proteomics service is ideal for long-term projects or projects with large sample sets which require accurate and reproducible quantitation.

Project Workflow

Pooled samples

Individual samples

Sample preparation

HPLC-UV Fractionation

LC-MS/MS DDA Analysis

DDA library generation and updates

LC-MS/MS DIA analysis

Quantitation and bioinformatics



[1]. 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.
[2]. Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villén J, MacCoss MJ. Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nat Commun. 2018 Dec 3;9(1):5128. doi: 10.1038/s41467-018-07454-w.

How to order

Request a Quote

Send us a no obligation request for quote and our dedicated sales team will reply to you within 24 hours.

Create an Online myBGI Account

Create a myBGI account to view all our sample and shipping documentation and to manage your project moving forwards. It's quick, free and easy!

Mass Spectrometry Service Specification

Label-Free DIA Quantitative Proteomics services are performed using nano-flow liquid chromatography and cutting-edge mass spectrometer (Q Exactive HF/HF-X and Orbitrap Fusion Lumos).

  • Sample Preparation and Services

    Sample Preparation and Services

    • The QC analysis of enzymatic hydrolysis is strictly controlled by LC-MS
    • DDA-Spectral Library generated using HPLC technology and sample fractionation
    • 2h/fraction for non blood; and 2h/fraction for non-human blood; 1h/fraction for human blood
  • Quality Standard

    Quality Standard

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

    Turn Around Time

    • Typical 4-5 weeks from sample QC acceptance to data report delivery

Sample Requirements

We accept protein samples in a variety of formats. For attaining maximum proteome coverage we recommend utilizing our sample fractionation services, performed using our off-line UHPLC-UV platform.

Sample type

Recommend Amount

Minimum Amount


Common animal tissues:
animal internal organs (heart, liver, spleen, lung, kidney), skin, muscle, brain, etc

≥ 5 mg


(Toxoplasma, Schistosomiasis, Drosophila, Acarid, Plutella xylostella, Laodelphax, Cestode, Cicada, Hematodinium, etc.)

≥ 5 mg


Suspended cells, adherent cells

≥ 1×10^7


Cell culture supernatant

≥ 5 mL


Exosome isolated by customer

≥ 20 µg, ≥ 0.5 µg/µL


Plasma, serum (remove highly-abundant protein)

≥ 200 µL


Plasma, serum (with highly-abundant protein)



Amniotic fluid, cerebrospinal fluid, semen, etc. (remove highly-abundant protein)

≥ 1 mL


Amniotic fluid, cerebrospinal fluid, semen, etc. (with highly-abundant protein)

≥ 200 µL


Saliva, milk

≥ 200 µL



≥ 30 mL



≥ 15 µL


Twigs of plants (leaf buds, tender leaves), algae

≥ 300 mg


Old leaves, roots, stems, bark of plants

≥ 1 g


Plant buds, pollen

≥ 100 mg


Plant seeds (rice/wheat seeds, etc.),
fruits (apples, peaches, pears)

≥ 1 g


Prokaryotic bacteria (E. coli, Staphylococcus aureus, etc.),
fungi (yeast, etc.)

Thallus ≥ 50 mg
cells ≥ 5×10^6

Protein solution

Complex protein solution, protein powder

≥ 40 µg,
≥ 0.5 µg/µL



≥ 300 mg

Data Analysis

Advanced Bioinformatics

  • Data analysis and validation performed with Mascot

  • Protein identification and quantification list

  • Differential proteins data statistics and volcano plot

  • Principal component analysis (PCA) and cluster analysis

  • Protein GO/COG/KOG/Pathway annotation

  • GO/COG/KOG enrichment analysis of differential proteins

  • Protein-protein interaction analysis

  • Protein subcellular localization analysis

  • Time series analysis

  • Repeatability analysis

  • Quantitative proteomics and phosphoproteomics correlation analysis


We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

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