Mascot target output for model construction (FDR=0.01):
(Example)
1. Run Mascot databases search at FDR=0.01, output the results file with .csv
format (result.csv), include pep-score and pep-ident.
2. Revise result.csv by deleting the column "prot-desc".
In addition, split the column "pep_scan_title" by using "text-to-column"
in Excel, create a column "RT/min" and put all retention times in this column.
Mascot target output for application (p=0.10):
(Example)
1. Run Mascot database search (target-decoy search) at p=0.10, output the
target file with .csv format (target.csv), include pep-score and pep-ident.
2. Revise target.csv by deleting the column "prot-desc".
In addition, split the column "pep_scan_title" by using "text-to-column"
in Excel, create a column "RT/min" and put all retention times in this column.
Mascot decoy output for application (p=0.10):
(Example)
3. Output the decoy file with .csv format (decoy.csv), include pep-score and
pep-ident.
4. Revise decoy.csv by deleting the column "prot-desc". In addition, split
the column "pep_scan_title" by using "text-to-column" in Excel, create a
column "RT/min" and put all retention times in this column.
q-value:
q value is equivalent to FDR but more robust and confident. It is defined as the minimal FDR at which a peptide spectra match (PSM) can be accepted. In practice, each PSM will be calculated a corresponding q value. The default q value threshold is 0.01. Users can specify a q value threshold at which all PSMs with a higher q value will be screened out.