Table 1. Comet Search Parameters for Each Data Set.
| PXD007058 (synthetic data set) | PXD000138 (synthetic data set) | PXD008355 (Arabidopsis data set) | PXD000612 (human data set) | |
|---|---|---|---|---|
| peptide mass tolerance | 20.0 ppm | 5 ppm | 7 ppm | 7 ppm |
| fragment bin tolerance | 0.02 Da | 0.02 Da | 0.02 Da | 0.02 Da |
| digest mode | tryptic | tryptic | tryptic | tryptic |
| max missed cleavages | 4 | 4 | 2 | 2 |
| fixed mods | carbamidomethylation (C) | carbamidomethylation (C) | carbamidomethylation (C) | carbamidomethylation (C) |
| variable mods | oxidation (MWP) | oxidation (M) | oxidation (M) | oxidation (M) |
| phospho (STYXa) | phospho (STYXa) | phospho (STYXa) | phospho (STYXa) | |
| pyrophospho (STY)b, N-terminal acetylation | N-terminal acetylation | N-terminal acetylation | N-terminal acetylation | |
| ammonia loss (QC) | ammonia loss (QC) | ammonia loss (QC) | ammonia loss (QC) | |
| pyro-Glu (EQ on the N-terminus) | pyro-Glu (EQ on the N-terminus) | pyro-Glu (EQ on the N-terminus) | pyro-Glu (EQ on the N-terminus) | |
| deamination (NQ) | deamination (NQ) | deamination (NQ) | deamination (NQ) | |
| max variable PTMs | 5 | 5 | 5 | 5 |
a
X corresponds to the different decoy amino acid searched: Ala, Gly, Leu, Asp, Glu, or Pro.
b
Preliminary analysis of the data set detected that several peptides had been manufactured with pyrophosphate modification rather than the intended phosphate, which can cause apparent errors when comparing the results to the answer key if they are not accounted for.