Parameter | Algorithm | |
X! Tandem | Omssa | |
Precursor charge state | +2 to +4 | +2 to +4 |
Enzyme | Trypsin | Trypsin |
Missed cleavages n | 2 | 2 |
Precursor mass error ppm | 25 | 25 |
Peptide mass error tolerance Da | 0.5 | 0.5 |
Fixed modifications | Carbamidomethylation on cysteine | Carbamidomethylation on cysteine |
Variable modifications | Asparagine/glutamine deamidation Methionine oxidation | Asparagine/glutamine deamidation Methionine oxidation |
FDR# % | 1 | 1 |
Average PSMs¶ n | 7877 | 6642 |
Average peptides¶ n | 1332 | 830 |
Average proteins¶ n | 524 | 412 |
FDR: false discovery rate; PSM: peptide spectral matches. #: for each algorithm the PSM were filtered based on a score threshold of 1% FDR, which was established using a decoy database search; ¶: the average parameters shown are average combined lists taken from the merged X! Tandem and merged Omssa data.