Question:
My protein was analyzed using Alphalyse’s Pick ‘n Post protein identification service. The sample gave very good MS data, but was not identified because it is a novel protein not yet present in the NCBI database. Can you provide me the raw MS peptide fingerprint spectra and MS/MS peptide sequence data for additional database searching?
Answer:
For unidentified proteins with good MS data, Alphalyse can provide Mascot Generic Format files (MGF files) containing the MS data that was used for the Mascot database search. The MGF files contain the peptide masses and the peptide fragment masses obtained for each sample in a format that can be uploaded to the Mascot database search software.
The MGF file will enable you to repeat the database search:
A) on your own in-house Mascot search engine with proprietary databases,
B) on the public Mascot server http://www.matrixscience.com/ when more protein sequences are added in the future, and
C) on other database search programs using different search algorithms.
Please contact Alphalyse at info@alphalyse.com for a price quotation on the MGF file conversion for your samples, and to obtain a small tutorial on how to perform the MGF Mascot database searches. Learn more about protein identification using mass spectrometry.
Filed under: Uncategorized Tagged: | Alphalyse, MALDI, mascot, mass spec, mass spec method, mass spectroscopy, ncbi, peptide, Pick-n-Post, protein, Protein Analysis, Protein ID, Protein Identification, Protein Mass Spec
