SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries.

ABSTRACT: The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative compa

SUBMITTER: Wu JX 

PROVIDER: S-EPMC4937520 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature