Table 1

Comparison of results reported by PLGS and PAnalyzer
Single Run #1 #2 #3 #4 #5
PLGS Hit 143 161 144 129 134
Protein 305 338 324 293 307
Conclusive 173 178 179 161 157
Indistinguishable 77 (29) 94 (39) 82 (32) 63 (26) 78 (31)
PAnalyzer Ambiguous group 0 4 (1) 12 (3) 0 18 (2)
Non-conclusive 55 62 51 69 54
Filtered 0 0 0 0 0
Multiple Run Th1 Th2 Th3 Th4 Th5
PLGS Hit - - - - -
Protein - - - - -
Conclusive 335 161 100 69 54
Indistinguishable 74 (37) 103 (38) 106 (33) 104 (31) 84 (28)
PAnalyzer Ambiguous group 11 (3) 9 (2) 12 (2) 11 (2) 24 (2)
Non-conclusive 98 81 82 66 65
Filtered 0 164 218 268 291

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 low confidence (red).

Prieto et al.

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

Open Data