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A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics

Liu, Hongbin, Sadygov, Rovshan G., Yates, John R.·2004·Analytical Chemistry

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Abstract

Proteomic analysis of complex protein mixtures using proteolytic digestion and liquid chromatography in combination with tandem mass spectrometry is a standard approach in biological studies. Data-dependent acquisition is used to automatically acquire tandem mass spectra of peptides eluting into the mass spectrometer. In more complicated mixtures, for example, whole cell lysates, data-dependent acquisition incompletely samples among the peptide ions present rather than acquiring tandem mass spectra for all ions available. We analyzed the sampling process and developed a statistical model to accurately predict the level of sampling expected for mixtures of a specific complexity. The model also predicts how many analyses are required for saturated sampling of a complex protein mixture. For a yeast-soluble cell lysate 10 analyses are required to reach a 95% saturation level on protein identifications based on our model. The statistical model also suggests a relationship between the level of sampling observed for a protein and the relative abundance of the protein in the mixture. We demonstrate a linear dynamic range over 2 orders of magnitude by using the number of spectra (spectral sampling) acquired for each protein.

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Authors: Liu, H., Sadygov, R. G., & Yates, J. R.
Venue: Analytical Chemistry
Publisher: American Chemical Society (ACS)
Published: 2004-06-02
Volume: 76
Issue: 14
Pages: 4193-4201
ISSN: 0003-2700 (ISSN-L)
1520-6882
DOI: 10.1021/ac0498563
OpenAlex: W1997504014
Cited by: 2,500
References: 2
FWCI: 38.86
Type: journal article
Language: en
Open access: closed

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A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics

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