title: SWATH-ID: An instrument method which combines identification and quantification in a single analysis.
abstract: 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.
authors.affiliation: SCIEX, Concord, ON, Canada.
authors.forename: Yang
authors.initials: Y
authors.lastname: Kang
authors.affiliation: SCIEX, Concord, ON, Canada.
authors.forename: Lyle
authors.initials: L
authors.lastname: Burton
authors.affiliation: SCIEX, Concord, ON, Canada.
authors.forename: Adam
authors.initials: A
authors.lastname: Lau
authors.affiliation: SCIEX, Concord, ON, Canada.
authors.forename: Stephen
authors.initials: S
authors.lastname: Tate
keywords: DIA; Peptide identification; Peptide quantitation; SWATH