For a Peptide Mass Fingerprint, the file should contain a list of peptide mass values, one per line. Mascot will treat the first numeric value on each line as a mass value, and ignore everything else. The peak list export formats of a wide range of instrument data systems are directly compatible with these requirements. In addition, Mascot will automatically recognise the PE Biosystems .PKM format and the Bruker Analysis Data Report from AutoXecute. Sciex API III A data file may include embedded search parameters .
Most embedded parameters can only appear once, at the head of the data file.
If there is a conflict between the values of the embedded parameters and values entered into search form fields, the embedded parameters always take precedence. The following paragraphs illustrate the data file format by means of examples. The rules which Mascot follows when parsing a data file provide an alternative, more rigorous description of what is and is not acceptable. In the case of a Peptide Mass Fingerprint, each query is just a single peptide mass value. If your MS data system outputs peak lists which include additional values, such as peak intensity, these will be ignored.