title: Expansion of the ion library for mining SWATH-MS data through fractionation proteomics.
abstract: The strategy of sequential window acquisition of all theoretical fragment ion spectra (SWATH) is emerging in the field of label-free proteomics. A critical consideration for the processing of SWATH data is the quality of the ion library (or mass spectrometric reference map). As the availability of open spectral libraries that can be used to process SWATH data is limited, most users currently create their libraries in-house. Herein, we propose an approach to construct an expanded ion library using the data-dependent acquisition (DDA) data generated by fractionation proteomics. We identified three critical elements for achieving a satisfactory ion library during the iterative process of our ion library expansion, including a correction of the retention times (RTs) gained from fractionation proteomics, appropriate integrations of the fractionated proteomics into an ion library, and assessments of the impact of the expanded ion libraries to data mining in SWATH. Using a bacterial lysate as an evaluation material, we employed sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to fractionate the lysate proteins and constructed the expanded ion library using the fractionation proteomics data. Compared with the ion library built from the unfractionated proteomics, approximately 20% more peptides were extracted from the expanded ion library. The extracted peptides, moreover, were acceptable for further quantitative analysis.
authors: Proteomics Division, BGI-Shenzhen , Beishan Industrial Zone, Yantian, Shenzhen, Guangdong 518083, China.
authors: Jin
authors: J
authors: Zi
authors: Shenyan
authors: S
authors: Zhang
authors: Ruo
authors: R
authors: Zhou
authors: Baojin
authors: B
authors: Zhou
authors: Shaohang
authors: S
authors: Xu
authors: Guixue
authors: G
authors: Hou
authors: Fengji
authors: F
authors: Tan
authors: Bo
authors: B
authors: Wen
authors: Quanhui
authors: Q
authors: Wang
authors: Liang
authors: L
authors: Lin
authors: Siqi
authors: S
authors: Liu
mesh_terms: D057225:Data Mining; D004591:Electrophoresis, Polyacrylamide Gel; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics