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Keck
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Protein Identification from DIGE Experiments
Protein Identification from DIGE
Experiments
Protein identification for DIGE
analysis is currently performed on an Applied Biosystems (AB) Model
4700 MALDI-Tof/Tof mass spectrometer. The NCBInr database is routinely
searched, with species specific database searches also available (note
that databases other than human, rat and mouse may be subject to the
database fee). Search parameters include a peptide mass accuracy of
50ppm, a MS/MS fragment accuracy of 0.2Da and variable modifications of
carbamidomethylcysteine (cysteines are alkylated prior to DIGE using
iodoacetamide), and methionine oxidation. Mascot database searching is
used with a combined peptide mass fingerprint and MS/MS search. DIGE
protein identification results are posted to the Yale Protein
Expression Database (YPED) for online viewing of identifications
relative to spot number and gel image.
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