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Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition

Li, Wenxue
Author Li, Wenxue Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
Chi, Hao
Author Chi, Hao Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
Salovska, Barbora
Author Salovska, Barbora Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
Wu, Chongde
Author Wu, Chongde Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
Sun, Liangliang
Author Sun, Liangliang Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
Rosenberger, George
Author Rosenberger, George Department of Systems Biology, Columbia University, New York, NY, USA
Liu, Yansheng
Author Liu, Yansheng ORCID Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA. yansheng.liu@yale.edu Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA. yansheng.liu@yale.edu

Journal of the American Society for Mass Spectrometry. 2019 Aug ; 30 (8) : 1396-1405. [epub] 20190530

J Am Soc Mass Spectrom
ISSN 1879-1123 | 1044-0305
Source

Language English Country United States Media print-electronic

Document type Journal Article

Persistent link https://www.medvik.cz/link/pmid31147889

PubMed 31147889
DOI 10.1007/s13361-019-02243-1
PII: 10.1007/s13361-019-02243-1
Knihovny.cz E-resources

Keywords
Data-independent acquisition, Isolation windows, Maxquant, Spectronaut, pFind,
MeSH
Chromatography, Reverse-Phase MeSH
Mass Spectrometry methods MeSH
Humans MeSH
Cell Line, Tumor MeSH
Peptides analysis MeSH
Proteins analysis MeSH
Proteomics methods MeSH
Software MeSH
Check Tag
Humans MeSH
Publication type
Journal Article MeSH
Names of Substances
Peptides MeSH
Proteins MeSH

Due to the technical advances of mass spectrometers, particularly increased scanning speed and higher MS/MS resolution, the use of data-independent acquisition mass spectrometry (DIA-MS) became more popular, which enables high reproducibility in both proteomic identification and quantification. The current DIA-MS methods normally cover a wide mass range, with the aim to target and identify as many peptides and proteins as possible and therefore frequently generate MS/MS spectra of high complexity. In this report, we assessed the performance and benefits of using small windows with, e.g., 5-m/z width across the peptide elution time. We further devised a new DIA method named RTwinDIA that schedules the small isolation windows in different retention time blocks, taking advantage of the fact that larger peptides are normally eluting later in reversed phase chromatography. We assessed the direct proteomic identification by using shotgun database searching tools such as MaxQuant and pFind, and also Spectronaut with an external comprehensive spectral library of human proteins. We conclude that algorithms like pFind have potential in directly analyzing DIA data acquired with small windows, and that the instrumental time and DIA cycle time, if prioritized to be spent on small windows rather than on covering a broad mass range by large windows, will improve the direct proteome coverage for new biological samples and increase the quantitative precision. These results further provide perspectives for the future convergence between DDA and DIA on faster MS analyzers.

Department of Chemistry Michigan State University East Lansing MI 48824 USA

Department of Genome Integrity Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

Department of Pharmacology Yale University School of Medicine New Haven CT 06520 USA

Department of Systems Biology Columbia University New York NY USA

Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences Institute of Computing Technology CAS Beijing China

Yale Cancer Biology Institute Yale University West Haven CT 06516 USA

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