PeptideClassifier for protein inference and targeted quantitative proteomics

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Figure 1: Schematic overview of where PeptideClassifier maps onto a shotgun proteomics workflow and selected applications.
Figure 2: Overview of the distinct peptide evidence classes of our classification scheme for eukaryotes and prokaryotes.

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Acknowledgements

We thank C. Panse for contributing a first XML parser to extract information from database search engine output files, E. Brunner and G. Hausmann for feedback on the manuscript and K. Basler, U. Grossniklaus, R. Aebersold, M. Hengartner and J. Jiricny for continued support of the Quantitative Model Organism Proteomics bioinformatics core group. E.Q. and C.H.A. are members of the Quantitative Model Organism Proteomics Initiative, which is supported by the University Research Priority Program Systems Biology/Functional Genomics of the University of Zurich.

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Correspondence to Christian H Ahrens.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–3, Supplementary Fig. 1 (PDF 329 kb)

Zipped file 1

Peptide Classifier_Auxiliary Scripts (ZIP 51001 kb)

Zipped file 2

Peptide Classifier_software code (ZIP 8160 kb)

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