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The Generation of a Comprehensive Spectral Library for the Analysis of the Guinea Pig Proteome by SWATH-MS

Lookup NU author(s): Dr Pawel PalmowskiORCiD, Rachael Horbury, Emeritus Professor Nick Europe-Finner, Dr Magdalena Karolczak-Bayatti, Dr Andrew Porter, Dr Achim Treumann, Professor Michael TaggartORCiD



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


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 pig (Cavia porcellus) is an excellent experimental model for translation to many aspects of human physiology and disease, yet there is limited experimental information regarding its proteome. To overcome this knowledge gap, a comprehensive spectral library of the guinea pig proteome is generated. Homogenates and tryptic digests are prepared from 16 tissues and subjected to >200 DDA runs. Analysis of >250 000 peptide‐spectrum matches resulted in a library of 73 594 peptides from 7666 proteins. Library validation is provided by i) analyzing externally derived SWATH files ( and comparing peptide intensity quantifications; ii) merging of externally derived data to the base library. This furnishes the research community with a comprehensive proteomic resource that will facilitate future molecular‐phenotypic studies using (re‐engaging) the guinea pig as an experimental model of relevance to human biology. The spectral library and raw data are freely accessible in the MassIVE repository (MSV000083199).

Publication metadata

Author(s): Palmowski P, Watson R, Europe-Finner GN, Karolczak-Bayatti M, Porter A, Treumann A, Taggart MJ

Publication type: Article

Publication status: Published

Journal: Proteomics

Year: 2019

Volume: 19

Issue: 15

Print publication date: 01/08/2019

Online publication date: 22/07/2019

Acceptance date: 13/07/2019

Date deposited: 23/07/2019

ISSN (print): 1615-9853

ISSN (electronic): 1615-9861

Publisher: Wiley-Blackwell Publishing Ltd.


DOI: 10.1002/pmic.201900156


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