title: Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.
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.
authors: Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, 61 Biopolis Drive, Singapore 138673.
authors: Jayantha
authors: J
authors: Gunaratne
authors: Alexander
authors: A
authors: Schmidt
authors: Andreas
authors: A
authors: Quandt
authors: Suat Peng
authors: SP
authors: Neo
authors: Omer Sinan
authors: OS
authors: Saraç
authors: Tannia
authors: T
authors: Gracia
authors: Salvatore
authors: S
authors: Loguercio
authors: Erik
authors: E
authors: Ahrné
authors: Rachel Li Hai
authors: RL
authors: Xia
authors: Keng Hwa
authors: KH
authors: Tan
authors: Christopher
authors: C
authors: Lössner
authors: Jürg
authors: J
authors: Bähler
authors: Andreas
authors: A
authors: Beyer
authors: Walter
authors: W
authors: Blackstock
authors: Ruedi
authors: R
authors: Aebersold
mesh_terms: D030562:Databases, Protein; D015966:Gene Expression Regulation, Fungal; D013058:Mass Spectrometry; D005810:Multigene Family; D010449:Peptide Mapping; D010455:Peptides / Q000302:isolation & purification*; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012568:Schizosaccharomyces / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029702:Schizosaccharomyces pombe Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction
chemical_list: D010455:Peptides; D020543:Proteome; D012333:RNA, Messenger; D029702:Schizosaccharomyces pombe Proteins