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Micro-flow LC-MS/MS Based Single Shot Proteomics

ABSTRACT: In this study, we systematically optimized the micro-flow LC-MS/MS system based ssDDA proteomics. Our results show that combination of 2 – 3 h gradient with prosit rescore method identified the highest number of proteins and peptides. There is no benefit to increase column length. A single 3 h run identified about 9,200 proteins from 50 µg of Arabidopsis protein digest. The micro-flow LC-MS/MS system based ssDDA proteomics can be widely used for routine proteomics analysis of large cohort samples.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human) Arabidopsis Thaliana (mouse-ear Cress) Mus Musculus (mouse)

TISSUE(S): Root, Cell Culture, Thymus, Small Intestine

SUBMITTER: Yangyang Bian

LAB HEAD: Bernhard Kuster

PROVIDER: PXD023587 | Pride | 2021-07-01

REPOSITORIES: Pride

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Identification of 7 000-9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC-MS/MS.

Bian Yangyang Y The Matthew M Giansanti Piero P Mergner Julia J Zheng Runsheng R Wilhelm Mathias M Boychenko Alexander A Kuster Bernhard B

Analytical chemistry 20210614 25

A current trend in proteomics is to acquire data in a "single-shot" by LC-MS/MS because it simplifies workflows and promises better throughput and quantitative accuracy than schemes that involve extensive sample fractionation. However, single-shot approaches can suffer from limited proteome coverage when performed by data dependent acquisition (ssDDA) on nanoflow LC systems. For applications where sample quantities are not scarce, this study shows that high proteome coverage can be obtained usin ...[more]

PMID: 34124897

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