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Accurate Precursor Mass Assignment Improves Peptide Identification in Data-Independent Acquisition Mass Spectrometry

Authors
Mun, Dong-GiNam, DowoonKim, HokeunPandey, AkhileshLee, Sang-Won
Issue Date
2-7월-2019
Publisher
AMER CHEMICAL SOC
Citation
ANALYTICAL CHEMISTRY, v.91, no.13, pp.8453 - 8460
Indexed
SCIE
SCOPUS
Journal Title
ANALYTICAL CHEMISTRY
Volume
91
Number
13
Start Page
8453
End Page
8460
URI
https://scholar.korea.ac.kr/handle/2021.sw.korea/64163
DOI
10.1021/acs.analchem.9b01474
ISSN
0003-2700
Abstract
Proteomics research today no longer simply seeks exhaustive protein identification; increasingly, it is also desirable to obtain robust, large-scale quantitative information. To accomplish this, data-independent acquisition (DIA) has emerged as a promising strategy largely owing to developments in advanced mass spectrometers and sophisticated data analysis methods. Nevertheless, the highly complex multiplexed MS/MS spectra produced by DIA remain challenging to interpret. Here, we present a novel strategy to analyze DIA data, based on unambiguous precursor mass assignment through the mPE-MMR (multiplexed post-experimental monoisotopic mass refinement) procedure and combined with complementary multistage database searching. Compared to conventional spectral library searching, the accuracy and sensitivity of peptide identification were significantly increased by incorporating precise precursor masses in DIA data. We demonstrate identification of additional peptides absent from spectral libraries, including sample-specific mutated peptides and post-translationally modified peptides using MS-GF+ and MODa/MODi multistage database searching. This first use of unambiguously determined precursor masses to mine DIA data demonstrates considerable potential for further exploitation of this type of experimental data.
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