Missed Cleavages Setting the number of allowed missed cleavage sites to zero simulates a limit digest. If you are confident that your digest is perfect, with no partial fragments present, this will give maximum discrimination and the highest score. If experience shows that your digest mixtures usually include some partials, that is, peptides with missed cleavage sites, you should choose a setting of 1, or maybe 2 missed cleavage sites. Don't specify a higher number without good reason, because each additional level of missed cleavages increases the number of calculated peptide masses to be matched against the experimental data. If the actual digest does not contain extended partials, this simply increases the number of random matches, and so reduces discrimination.
Data file Enter the path to a data file containing mass data.
Details of the file format can be found here . If a file name is present in this field, any contents in the Query window are ignored. The contents of the query window are only used when no data file has been specified . For a Peptide Mass Fingerprint, the query window must contain a list of peptide mass values, one per line. Anything after the first numeric value on each line is ignored.