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  Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant

Chen, Z. A., Fischer, L., Cox, J., & Rappsilber, J. (2016). Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant. Molecular and Cellular Proteomics, 15(8), 2769-2778. doi:10.1074/mcp.M115.056481.

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 Urheber:
Chen, Zhuo A.1, Autor
Fischer, Lutz1, Autor
Cox, Jürgen2, Autor           
Rappsilber, Juri1, Autor
Affiliations:
1external, ou_persistent22              
2Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society, ou_2063284              

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Schlagwörter: MASS-SPECTROMETRY; PROTEOMICS; QUANTIFICATION; IDENTIFICATIONBiochemistry & Molecular Biology;
 Zusammenfassung: The conceptually simple step from cross-linking/mass spectrometry (CLMS) to quantitative cross-linking/mass spectrometry (QCLMS) is compounded by technical challenges. Currently, quantitative proteomics software is tightly integrated with the protein identification workflow. This prevents automatically quantifying other m/z features in a targeted manner including those associated with crosslinked peptides. Here we present a new release of MaxQuant that permits starting the quantification process from an m/z feature list. Comparing the automated quantification to a carefully manually curated test set of cross-linked peptides obtained by cross-linking C3 and C3b with BS3 and isotope-labeled BS3-d4 revealed a number of observations: (1) Fully automated process using MaxQuant can quantify cross-links in our reference data set with 68% recall rate and 88% accuracy. (2) Hidden quantification errors can be converted into exposed failures by label-swap replica, which makes label-swap replica an essential part of QCLMS. (3) Cross-links that failed during automated quantification can be recovered by semi-automated re-quantification. The integrated workflow of MaxQuant and semi-automated assessment provides the maximum of quantified cross-links. In contrast, work on larger data sets or by less experienced users will benefit from full automation in MaxQuant.

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Sprache(n): eng - English
 Datum: 2015-10-152016-06-142016-08-01
 Publikationsstatus: Erschienen
 Seiten: 10
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: ISI: 000380809100017
DOI: 10.1074/mcp.M115.056481
 Art des Abschluß: -

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Titel: Molecular and Cellular Proteomics
Genre der Quelle: Zeitschrift
 Urheber:
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Ort, Verlag, Ausgabe: Bethesda, MD : American Society for Biochemistry and Molecular Biology
Seiten: - Band / Heft: 15 (8) Artikelnummer: - Start- / Endseite: 2769 - 2778 Identifikator: ISSN: 1535-9476
CoNE: https://pure.mpg.de/cone/journals/resource/111035577487002