Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Mascot training exercises

Within each topic, the exercises become progressively more difficult, so are intended to be undertaken in order.

If you find an exercise too difficult, first follow the link for hints. If these don’t help, or there aren’t any, and you are really stuck, there may be a link to example search results.

Search Parameters

  1. Simple Peptide Mass Fingerprint: PMF1
  2. Tricky Peptide Mass Fingerprint: PMF2
  3. Difficult Peptide Mass Fingerprint: PMF3
  4. Peptide Mass Fingerprint mixture: PMF4
  5. MS/MS Search of ETD data: MSMS6


  1. Error Tolerant Search: MSMS1
  2. Phosphopeptides: MSMS5
  3. High precursor accuracy: MSMS7

Scoring & Statistics

  1. Target-decoy search: MSMS2

Very Large Searches

  1. Exporting search results: MSMS3

Mascot Distiller

  1. PMF: DIS1
  2. MS/MS: DIS2

Sequence Query

  1. Easy sequence tag: SQ1
  2. Tricky sequence tag: SQ2
  3. Distiller Search Toolbox: SQ3

Mascot Daemon

  1. Data dependent follow-up task: DM1


  1. iTRAQ quantitation: MSMS4
  2. SILAC quantitation: DIS3

Sequence Database Administration

  1. Configure AA Database: ADM1
  2. Configure NA Database: ADM2

Mascot System Administration

  1. Configure Mascot Security: ADM3