Open AccessQuantitative shotgun proteome analysis by direct infusion
Author(s) -
Jesse G. Meyer,
Natalie M. Niemi,
David J. Pagliarini,
Joshua J. Coon
Publication year - 2020
Publication title -
nature methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 19.469
H-Index - 318
eISSN - 1548-7105
pISSN - 1548-7091
DOI - 10.1038/s41592-020-00999-z
Subject(s) - proteome , shotgun proteomics , shotgun , mass spectrometry , proteomics , biomarker discovery , chromatography , label free quantification , chemistry , peptide , fractionation , tandem mass spectrometry , computational biology , quantitative proteomics , biology , biochemistry , gene
Liquid chromatography-mass spectrometry (LC-MS) delivers sensitive peptide analysis for proteomics but requires extensive analysis time, reducing throughput. Here, we demonstrate that gas-phase peptide separation instead of LC enables fast proteome analysis. Using direct infusion-shotgun proteome analysis (DI-SPA) by data-independent acquisition mass spectrometry (DIA-MS), we demonstrate the targeted quantification of over 500 proteins within minutes of MS data collection (~3.5 proteins per second). We show the utility of this technology in performing a complex multifactorial proteomic study of interactions between nutrients, genotype and mitochondrial toxins in a collection of cultured human cells. More than 45,000 quantitative protein measurements from 132 samples were achieved in only ~4.4 h of MS data collection. Enabling fast, unbiased proteome quantification without LC, DI-SPA offers an approach to boost throughput, critical to drug and biomarker discovery studies that require analysis of thousands of proteomes.