Table 3. Accurate mass and time tag data summary.

AMT tag database statistics for both the 2003 HUPO-Dec_Submission set and the 2004 HUPO-Jul_Submission set. High matched confidence was defined here as an AMT tag measured in at least 2 of 3 triplicates. Unique peptide-protein pairs are those peptides that map to a single protein.

AMT tag Date Results Type	HUPO- Dec_Submissiona	HUPO- Jul_Submissionb
All Possible Peptide-Protein Pairs	4473	2806
High Matched Confidence Peptide- Protein Pairs	2811	2298
Unique Peptide-Protein pairs	2802	1493
High Matched Confidence Unique Peptides	1704	1225
All Putative Proteins	2625	842
High Matched Confidence Proteins	1366	585

^aSEQUEST peptide identification criteria used previously with the AMT approach for microbial systems [22,30] with peptide identifications from [15].

^bSEQUEST filters with more stringent cut-offs, at least partially tryptic and a minimum DelCN of 0.1 with +1, +2, and +3 charge states using minimum XCorr values of 1.9, 2.2, 3.75 respectively with peptide identifications from [15] and [17].