Open Access Software

PAnalyzer: A software tool for protein inference in shotgun proteomics

Gorka Prieto1*, Kerman Aloria2, Nerea Osinalde3, Asier Fullaondo4, Jesus M Arizmendi3 and Rune Matthiesen5

Author Affiliations

1 Department of Communications Engineering, University of the Basque Country (UPV/EHU), Alda. Urquijo s/n, Bilbao, 48013, Spain

2 Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain

3 Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain

4 Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain

5 Proteolysis in diseases, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-465, Portugal

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BMC Bioinformatics 2012, 13:288  doi:10.1186/1471-2105-13-288

Published: 5 November 2012

Additional files

Additional file 1:

Sample CSV output file. The output report in CSV format for the HEK 293T sample analysis using as input five replicate runs. Peptide score threshold has been selected as red (low confidence) and runs threshold as 3 (identification in at least 3 replicates).

Format: CSV Size: 302KB Download file

Open Data

Additional file 2:

Sample HTML output file. The output report in HTML format for the HEK 293T sample analysis using as input five replicate runs. Peptide score threshold has been selected as red (low confidence) and runs threshold as 3 (identification in at least 3 replicates).

Format: HTML Size: 1.4MB Download file

Open Data

Additional file 3:

Sample mzIdentML output file. The output report in mzIdentML v1.1.0 format for the Mascot MS/MS analysis example provided by the HUPO-PSI group.

Format: MZID Size: 297KB Download file

Open Data

Additional file 4:

Results reported by PLGS and PAnalyzer filtering low confidence peptides. Total protein extracts from HEK 293T cells have been analyzed in 5 replicate runs. In single run analysis, the number at the top row indicates the run identifier, while in multiple run analysis the number indicates the runs threshold. ProteinLynx Global Server rows show the number of hits and proteins reported, while the PAnalyzer rows show the number of proteins reported in the different evidence categories presented in the paper. The number of groups are indicated in parenthesis in the case of indistinguishable and ambiguous proteins. ProteinLynx Global Server (PLGS) cannot perform multiple run analysis. The peptide score filter is medium confidence (yellow).

Format: CSV Size: 1KB Download file

Open Data

Additional file 5:

Additional file 5: Results reported by PLGS and PAnalyzer with only high confidence peptides. Total protein extracts from HEK 293T cells have been analyzed in 5 replicate runs. In single run analysis, the number at the top row indicates the run identifier, while in multiple run analysis the number indicates the runs threshold. ProteinLynx Global Server rows show the number of hits and proteins reported, while the PAnalyzer rows show the number of proteins reported in the different evidence categories presented in the paper. The number of groups are indicated in parenthesis in the case of indistinguishable and ambiguous proteins. ProteinLynx Global Server (PLGS) cannot perform multiple run analysis. The peptide score filter is high confidence (green).

Format: CSV Size: 1KB Download file

Open Data