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SWATH‐ID: An instrument method which combines identification and quantification in a single analysis
Author(s) -
Kang Yang,
Burton Lyle,
Lau Adam,
Tate Stephen
Publication year - 2017
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201500522
Subject(s) - computer science , fragmentation (computing) , identification (biology) , peptide , data acquisition , window (computing) , fragment (logic) , computational biology , data mining , chemistry , biology , algorithm , biochemistry , world wide web , botany , operating system
Data‐independent acquisition (DIA) approaches, such as SWATH ® ‐MS, are showing great potential to reliably quantify significant numbers of peptides and proteins in an unbiased manner. These developments have enhanced interest in developing a single DIA method that integrates qualitative and quantitative analysis, eliminating the need of a prebuilt library of peptide spectra, which are created through data‐dependent acquisition methods or from public repositories. Here, we introduce a new DIA approach, referred to as “SWATH‐ID,” which was developed to allow peptide identification as well as quantitation. The SWATH‐ID method is composed of small Q1 windows, achieving better selectivity and thus significantly improving high‐confidence peptide extractions from data files. Furthermore, the SWATH‐ID approach transmits precursor ions without fragmentation as well as their fragments within the same SWATH acquisition period. This provides a single scan that includes all precursor ions within the isolation window as well as a record of all of their fragment ions, substantially negating the need for a survey scan. In this way all precursors present in a small Q1 window are associated with their fragment ions, improving the identification specificity and providing a more comprehensive and in‐depth view of protein and peptide species in complex samples.