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Database searching parameter settings for pFind and Maxquant programs.
| pFind | Maxquant | |
|---|---|---|
| Database | UniProt human protein database | |
| Mass tolerance | 5 ppm | 6 ppm |
| MS/MS tolerance | 0.02 Da | 50 ppm |
| Maximum missed cleavages | 3 | |
| Fixed modification | Carbamidomethyl[C] | |
| Variable modification | Acetyl[ProteinN-term] Oxidation[M] Methyl[K] Dimethyl[K] Trimethyl[K] |
|
| FDR filter | 0.01 peptide 0.01 protein |
0.01 PSM 0.01 protein 0.01 site |
