Gunaratne, J; Schmidt, A; Quandt, A; Neo, SP; Saraç, OS; Gracia, T; Loguercio, S; ... Aebersold, R; + view all Gunaratne, J; Schmidt, A; Quandt, A; Neo, SP; Saraç, OS; Gracia, T; Loguercio, S; Ahrné, E; Xia, RL; Tan, KH; Lössner, C; Bähler, J; Beyer, A; Blackstock, W; Aebersold, R; - view fewer (2013) Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas. Molecular & Cellular Proteomics , 12 (6) 1741 -1751. 10.1074/mcp.M112.023754.

Preview	Text Mol_Cell_Proteomics-2013-Gunaratne-1741-51.pdf Download (2MB)
	Text (Supplemental Figures S1-8) mcp.M112.023754-1.pdf Download (10MB)
Preview	Text ( Table S11. GO molecular function enrichments (p-value < 0.1) for undetected proteins in S. pombe with high (Top 25% quantile), medium (middle 50% quantile) and low (bottom 25% quantile) mRNA concentration. ) mcp.M112.023754-12.pdf Download (198kB)
	Text (Table S1. All identified proteins and peptides including human orthologs ) mcp.M112.023754-2.xls Download (1MB)
	Text ( Table S2: List of all identified peptide per protein ranked by the number of PSM ) mcp.M112.023754-3.xls Download (10MB)
	Text ( Table S3. List of all peptide spectrum matches ) mcp.M112.023754-4.xls Download (6MB)
	Text (Table S4. Transitions of peptides overlappping with the S. Pombe PeptideAtlas downloaded for different MS-platforms from www.srmatlas.org ) mcp.M112.023754-5.xls Download (321kB)
	Text (Table S5. GO-term bias analysis of identified proteins ) mcp.M112.023754-6.xls Download (37kB)
	Text (Table S6. Determined emPAI values for proliferating cells from experiment 2 (Figure 1A) and comparison to the recently published dataset by Marguert et al. 2012 (Cell) ) mcp.M112.023754-7.xls Download (851kB)
	Text (Table S7. Correlation of determined emPAI and recently published copies per cell levels for 20 proteins ) mcp.M112.023754-8.xls Download (34kB)
	Text (Table S8. Functional protein annotation for protein clusters of different abundance ) mcp.M112.023754-9.xls Download (74kB)
	Text (Table S9: KEGG Pathway entry (Cell Cycle) (PATHWAY: spo04111) ) mcp.M112.023754-10.xls Download (31kB)
	Text ( Table S10. Determined emPAI values and mRNA expression for proliferating cells (Figure 4) ) mcp.M112.023754-11.xls Download (374kB)
	Text (Table S12. List of S. cerevisiae and human orthologs inlcuding protein abundance levels) mcp.M112.023754-13.xls Download (2MB)

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 r(s) >0.80 for proteins involved in translation to r(s) <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 publicly 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.

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