2019
DOI: 10.1002/pmic.201900156
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The Generation of a Comprehensive Spectral Library for the Analysis of the Guinea Pig Proteome by SWATH‐MS

Abstract: Advances in liquid chromatography‐mass spectrometry have facilitated the incorporation of proteomic studies to many biology experimental workflows. Data‐independent acquisition platforms, such as sequential window acquisition of all theoretical mass spectra (SWATH‐MS), offer several advantages for label‐free quantitative assessment of complex proteomes over data‐dependent acquisition (DDA) approaches. However, SWATH data interpretation requires spectral libraries as a detailed reference resource. The guinea pi… Show more

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Cited by 14 publications
(14 citation statements)
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“…1%, modified peptides excluded, extraction window: 10 min, XIC width: 10 ppm). The mouse heart spectral library was obtained from ProteomeXchange (Vizcaíno et al, 2014) (PXD017795, MSV000085036) and pre-aligned to a randomly selected SWATH file, as described (Palmowski et al, 2019). The results were exported, via MarkerView 1.2.1 (AB Sciex), as tab-separated ASCII files and processed using the Perseus software framework (Tyanova et al, 2016).…”
Section: Discussionmentioning
confidence: 99%
“…1%, modified peptides excluded, extraction window: 10 min, XIC width: 10 ppm). The mouse heart spectral library was obtained from ProteomeXchange (Vizcaíno et al, 2014) (PXD017795, MSV000085036) and pre-aligned to a randomly selected SWATH file, as described (Palmowski et al, 2019). The results were exported, via MarkerView 1.2.1 (AB Sciex), as tab-separated ASCII files and processed using the Perseus software framework (Tyanova et al, 2016).…”
Section: Discussionmentioning
confidence: 99%
“…This large proteome database provides an important foundation for future studies using chicken. A recent study has demonstrated the usefulness of merging published spectral libraries with other tissue specific libraries to discover more novel quantitative data from pre-acquired SWATH-MS files 18 , 46 , which would be technically impossible using conventional proteomics appraoch.…”
Section: Discussionmentioning
confidence: 99%
“…The generation of a spectral library assists the construction of a Data-independent acquisition (DIA) approach, in particular, a sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) that allows reproducible and precise quantification of thousands of proteins in complex tissue 18 . New biological insights have been made possible by combination and reutilization of open-access retinal spectral libraries for interrogation by SWATH‐MS recently 19 .…”
Section: Background and Summarymentioning
confidence: 99%