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To parse a Mascot identification result file (.dat file), user should define some settings. 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.

• Report Top
  • Absolute : absolute number of hits (protein groups) to identify
  • Auto : return hits (protein groups) with significant scores specifying a p value.
• Peptides cutoff
  • Ion with score less than the ion score cutoff are ignored.
• Subset
  • 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)
• Read sequence parser proerties :
  • Specify the rule to use to read protein sequence: get sequence only if present in identification result file, get sequence from mascot server for master proteins if necessary, get sequence from mascot server for all proteins. The latest mode may be long as a server connection will occured for almost all proteins

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”