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Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-25894
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dc.contributor.authorFahrner, Matthias-
dc.contributor.authorKook, Lucas-
dc.contributor.authorFröhlich, Klemens-
dc.contributor.authorBiniossek, Martin L.-
dc.contributor.authorSchilling, Oliver-
dc.date.accessioned2022-10-28T13:14:19Z-
dc.date.available2022-10-28T13:14:19Z-
dc.date.issued2021-
dc.identifier.issn2227-7382de_CH
dc.identifier.urihttps://digitalcollection.zhaw.ch/handle/11475/25894-
dc.description.abstractLiquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventional settings, such as fully specific enzymatic constraints. Here we evaluated the impact of the fragment mass tolerance in combination with the enzymatic constraints on the performance of three search engines. Three open-source search engines (Myrimatch, X! Tandem, and MSGF+) were evaluated concerning the suitability in semi- and unspecific searches as well as the importance of accurate fragment mass spectra in non-specific peptide searches. We then performed a semispecific reanalysis of the published NCI-60 deep proteome data applying the most suited parameters. Semi- and unspecific LC-MS/MS data analyses particularly benefit from accurate fragment mass spectra while this effect is less pronounced for conventional, fully specific peptide-spectrum matching. Search speed differed notably between the three search engines for semi- and non-specific peptide-spectrum matching. Semispecific reanalysis of NCI-60 proteome data revealed hundreds of previously undescribed N-terminal peptides, including cases of proteolytic processing or likely alternative translation start sites, some of which were ubiquitously present in all cell lines of the reanalyzed panel. Highly accurate MS2 fragment data in combination with modern open-source search algorithms enable the confident identification of semispecific peptides from large proteomic datasets. The identification of previously undescribed N-terminal peptides in published studies highlights the potential of future reanalysis and data mining in proteomic datasets.de_CH
dc.language.isoende_CH
dc.publisherMDPIde_CH
dc.relation.ispartofProteomesde_CH
dc.rightshttps://creativecommons.org/licenses/by/4.0/de_CH
dc.subjectNCI-60 reanalysisde_CH
dc.subjectEndogenous proteolysisde_CH
dc.subjectFragment mass tolerancede_CH
dc.subjectMass spectrometryde_CH
dc.subjectSemispecific peptide searchde_CH
dc.subject.ddc572: Biochemiede_CH
dc.titleA systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell linesde_CH
dc.typeBeitrag in wissenschaftlicher Zeitschriftde_CH
dcterms.typeTextde_CH
zhaw.departementSchool of Engineeringde_CH
zhaw.organisationalunitInstitut für Datenanalyse und Prozessdesign (IDP)de_CH
dc.identifier.doi10.3390/proteomes9020026de_CH
dc.identifier.doi10.21256/zhaw-25894-
dc.identifier.pmid34070654de_CH
zhaw.funding.euNode_CH
zhaw.issue2de_CH
zhaw.originated.zhawYesde_CH
zhaw.pages.start26de_CH
zhaw.publication.statuspublishedVersionde_CH
zhaw.volume9de_CH
zhaw.publication.reviewPeer review (Publikation)de_CH
zhaw.author.additionalNode_CH
zhaw.display.portraitYesde_CH
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Fahrner, M., Kook, L., Fröhlich, K., Biniossek, M. L., & Schilling, O. (2021). A systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines. Proteomes, 9(2), 26. https://doi.org/10.3390/proteomes9020026
Fahrner, M. et al. (2021) ‘A systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines’, Proteomes, 9(2), p. 26. Available at: https://doi.org/10.3390/proteomes9020026.
M. Fahrner, L. Kook, K. Fröhlich, M. L. Biniossek, and O. Schilling, “A systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines,” Proteomes, vol. 9, no. 2, p. 26, 2021, doi: 10.3390/proteomes9020026.
FAHRNER, Matthias, Lucas KOOK, Klemens FRÖHLICH, Martin L. BINIOSSEK und Oliver SCHILLING, 2021. A systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines. Proteomes. 2021. Bd. 9, Nr. 2, S. 26. DOI 10.3390/proteomes9020026
Fahrner, Matthias, Lucas Kook, Klemens Fröhlich, Martin L. Biniossek, and Oliver Schilling. 2021. “A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines.” Proteomes 9 (2): 26. https://doi.org/10.3390/proteomes9020026.
Fahrner, Matthias, et al. “A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines.” Proteomes, vol. 9, no. 2, 2021, p. 26, https://doi.org/10.3390/proteomes9020026.


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