Exercise MSMS7: Answers

1. What are suitable search parameters?

   Enzyme : Trypsin/P
   Fixed modifications : Carbamidomethyl (C)
   Variable modifications : Oxidation (M),Carbamidomethyl (N-term)
   Mass values : Monoisotopic
   Protein Mass : Unrestricted
   Peptide Mass Tolerance : ± 300 ppm
   Fragment Mass Tolerance: ± 500 ppm
   Max Missed Cleavages : 2
   Instrument type : ESI-QUAD-TOF

2. What advice would you give to the person who prepared the sample?

   Use less aggressive alkylation conditions or a different reagent

3. What advice would you give to the mass spectrometer operator?

   Calibrate your instrument. Looks to be capable of 20 ppm accuracy

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