Rescuing discarded spectra: full comprehensive analysis of a minimal proteome

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  • dc.contributor.author Lluch-Senar, Maria 1982-ca
  • dc.contributor.author Mancuso, Francesco M.ca
  • dc.contributor.author Climente González, Héctorca
  • dc.contributor.author Peña Paz, Marcia I.ca
  • dc.contributor.author Sabidó Aguadé, Eduard, 1981-ca
  • dc.contributor.author Serrano Pubull, Luis, 1982-ca
  • dc.date.accessioned 2016-04-14T16:10:58Z
  • dc.date.available 2016-04-14T16:10:58Z
  • dc.date.issued 2016
  • dc.description.abstract A common problem encountered when performing large-scale MS proteome analysis is the loss of information due to the high percentage of unassigned spectra. To determine the causes behind this loss we have analyzed the proteome of one of the smallest living bacteria that can be grown axenically, Mycoplasma pneumoniae (729 ORFs). The proteome of M. pneumoniae cells, grown in defined media, was analyzed by MS. An initial search with both Mascot and a species-specific NCBInr database with common contaminants (NCBImpn), resulted in around 79% of the acquired spectra not having an assignment. The percentage of non-assigned spectra was reduced to 27% after re-analysis of the data with the PEAKS software, thereby increasing the proteome coverage of M. pneumoniae from the initial 60% to over 76%. Nonetheless, 33 413 spectra with assigned amino acid sequences could not be mapped to any NCBInr database protein sequence. Approximately, 1% of these unassigned peptides corresponded to PTMs and 4% to M. pneumoniae protein variants (deamidation and translation inaccuracies). The most abundant peptide sequence variants (Phe-Tyr and Ala-Ser) could be explained by alterations in the editing capacity of the corresponding tRNA synthases. About another 1% of the peptides not associated to any protein had repetitions of the same aromatic/hydrophobic amino acid at the N-terminus, or had Arg/Lys at the C-terminus. Thus, in a model system, we have maximized the number of assigned spectra to 73% (51 453 out of the 70 040 initial acquired spectra).ca
  • dc.description.sponsorship This work was sup-ported by the European Research Council (ERC), the Fundación Marcelino Botín, the Spanish Ministerio de Economía y Com-petitividad BIO2007-61762 and the ISCIII (PI10/01702). TheCRG/UPF Proteomics Unit is part of the “Plataforma de Re-cursos Biomoleculares y Bioinform´aticos (ProteoRed)” supportedby grant PT13/0001 of Instituto de Salud Carlos III (ISCIII).We acknowledge the support of the Spanish Ministry of Economyand Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’, SEV-2012-0208. This project has received funding fromthe European Union’s Horizon 2020 research and innovationprogram under grant agreement No 634942
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L. Rescuing discarded spectra: full comprehensive analysis of a minimal proteome. Proteomics. 2016; 16(4): 554-563. DOI 10.1002/pmic.201500187ca
  • dc.identifier.doi http://dx.doi.org/10.1002/pmic.201500187
  • dc.identifier.issn 1615-9853
  • dc.identifier.uri http://hdl.handle.net/10230/26099
  • dc.language.iso engca
  • dc.publisher Wiley-VCH Verlagca
  • dc.relation.ispartof Proteomics. 2016; 16(4): 554-563
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2007-61762
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV-2012-0208
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/634942
  • dc.rights © 2016 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L. Rescuing discarded spectra: full comprehensive analysis of a minimal proteome. Proteomics. 2016; 16(4): 554-563ca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.subject.keyword MS
  • dc.subject.keyword Protein Identification
  • dc.subject.keyword Proteome coverage
  • dc.subject.keyword PTM
  • dc.subject.keyword Systems biology
  • dc.subject.keyword Translational errors
  • dc.subject.keyword Unassigned spectra
  • dc.subject.other Proteòmicaca
  • dc.subject.other Proteïnesca
  • dc.title Rescuing discarded spectra: full comprehensive analysis of a minimal proteomeca
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/acceptedVersionca

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