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Elsevier, Molecular and Cellular Proteomics, 6(12), p. 1741-1751, 2013

DOI: 10.1074/mcp.m112.023754

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Extensive Mass Spectrometry-based Analysis of the Fission Yeast Proteome: THE SCHIZOSACCHAROMYCES POMBE PeptideAtlas*

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Data provided by SHERPA/RoMEO

Abstract

We report a high-quality and system-wide proteome catalogue covering 71% (3,542 proteins) of the predicted genes of fission yeast, Schizosaccharomyces pombe, presenting the largest protein dataset to date for this important model organism. We obtained this high proteome and peptide (11.4 peptides/protein) coverage by a combination of extensive sample fractionation, high-resolution Orbitrap mass spectrometry and combined database searching using the iProphet software as part of the Trans- Proteomics Pipeline. All raw and processed data are made accessible in the S. pombe PeptideAtlas. The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances. The high coverage of the PeptideAtlas allowed correlation with transcriptomic data in a system-wide manner indicating that post-transcriptional processes control the levels of at least half of all identified proteins. Interestingly, the correlation was not equally tight for all functional categories ranging from rs>0.80 for proteins involved in translation to rs<0.45 for signal transduction proteins. Moreover, many proteins involved in DNA damage repair could not be detected in the PeptideAtlas despite their high mRNA levels, strengthening the translation-on-demand hypothesis for members of this protein class. In summary, the extensive and public available S. pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth and quantitative proteomic studies on this microorganism.