PAnalyzer: A software tool for protein inference in shotgun proteomics

BMC Bioinformatics

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).

ISSN: 1471-2105