When opening a Mascot identification file (dat file), user should specifiy parameters for Mascot parse. Indeed, the first mandatory step is to parse the dat file using free of charge parser distributed by Matrix Science.

A dialog box allow user to define parse setting. These parameters are the same as the one you can specify in Mascot Search engine. Mascot will use these informations in order to build the report.

• Absolute : absolute number of hits to identify
• Auto : return hits with significant scores

Ion with score less than the ion score cutoff are ignored.

Subset threshold definition: fractions core for a protein to be counted as a subset. Its score must be equal or greater than
Master_protein_score * (1-subset threshold)

If subset threshold is set to 1
*Score for a protein to be counted as a subset must be ≥ Master_protein_score * (1-1)
*Score for a protein to be counted as a subset must be ≥ Master_protein_score * (0)
*Score for a protein to be counted as a subset must be ≥ 0

All proteins sharing at least one peptide with the Master protein are counted as subsets

If subset threshold is set to 0
*Score for a protein to be counted as a subset must be ≥ Master_protein_score * (1-0)
*Score for a protein to be counted as a subset must be ≥ Master_protein_score * (1)
*Score for a protein to be counted as a subset must be ≥ Master_protein_score

No protein appears as a subset
This option can be problematical in case of further protein grouping

If subset threshold is set to 0.5 Score for a protein to be counted as a subset must be ≥ Master_protein_score * (1-0.5)
Score for a protein to be counted as a subset must be ≥ Master_protein_score * (0.5)
Score for a protein to be counted as a subset must be ≥ Master_protein_score/2

Only proteins whose score is at least equal to half of Master protein score are counted as subsets.
This option allows to limit the list of subset proteins to those which can be considered are the “more likely to be actually present in the sample”