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).

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Prieto et al. BMC Bioinformatics 2012 13:288   doi:10.1186/1471-2105-13-288