Generation of a mouse SWATH-MS spectral library to quantify 10148 proteins involved in cell reprogramming
Whetton, Anthony D
Graham, R. L. J.
AffiliationClinical Proteomics Research Group, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road Manchester, Manchester, U
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AbstractMurine models are amongst the most widely used systems to study biology and pathology. Targeted quantitative proteomic analysis is a relatively new tool to interrogate such systems. Recently the need for relative quantification on hundreds to thousands of samples has driven the development of Data Independent Acquisition methods. One such technique is SWATH-MS, which in the main requires prior acquisition of mass spectra to generate an assay reference library. In stem cell research, it has been shown pluripotency can be induced starting with a fibroblast population. In so doing major changes in expressed proteins is inevitable. Here we have created a reference library to underpin such studies. This is inclusive of an extensively documented script to enable replication of library generation from the raw data. The documented script facilitates reuse of data and adaptation of the library to novel applications. The resulting library provides deep coverage of the mouse proteome. The library covers 29519 proteins (53% of the proteome) of which 7435 (13%) are supported by a proteotypic peptide.
CitationUlanga U, Russell M, Patassini S, Brazzatti J, Graham C, Whetton AD, et al. Generation of a mouse SWATH-MS spectral library to quantify 10148 proteins involved in cell reprogramming. Sci Data. 2021 Apr 26;8(1).
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