Exercise MSMS3
Topic
Use a second pass search to find unusual modifications, sequence variants, and
non-specific cleavage.
Experimental
Search the supplied MGF format peak list against Swiss-Prot with a taxonomy filter of Mammalia.
Use Trypsin, 2 missed cleavages, 0.5 Da / 0.5 Da, no modifications in the first pass search, and ESI-QUAD-TOF ion series.
In X!Tandem, configure model refinement. In Mascot, check the search form option for an automatic error tolerant search
Data
Right-click this link:
MSMS3.mgf,
and choose Save to file
Tips
- If SwissProt not available, search a mix of mammalian proteins.
Questions
- Try to explain as many as possible of the additional error tolerant matches
- Are there any that you cannot explain or do not believe?
- Which modifications, if any, might you include in the first pass search?
Hints |
Mascot results |
Answers
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