Guide to identification of novel proteins not in public databases

Dec 2. 2014


I recently used Alphalyse’s protein identification service to analyze my protein. The sample gave me very good MS data. However it did not identify the protein because it is a novel protein not yet present in the NCBI database. Can you also provide me with the raw MS peptide fingerprinting spectra and MS/MS peptide sequence data? I need this for additional database searching.


For unidentified proteins with good MS data, Alphalyse can provide Mascot Generic Format files (MGF files). They contain the MS data used for the Mascot database search. More specifically, the MGF files contain the peptide masses and the peptide fragment masses obtained for each sample. The files are in a format that you can upload to the database search software.

With the MGF file you can repeat then the database search:

A) on your own in-house Mascot search engine with proprietary databases,

B) on the public server when more protein sequences are added in the future, and

C) on other database search programs using different search algorithms.

Please contact Alphalyse at for a price quotation on the MGF file conversion for your samples. We can also provide you with a small tutorial on how to perform the MGF Mascot database searches. Learn more about protein identification using mass spectrometry.

About Alphalyse

Alphalyse uses expertise in the field of protein chemistry and bioinformatics, combined with top-of-the-line mass spectrometry equipment, to provide protein analysis services globally.

Alphalyse aims to deliver high quality data and customer service to all of our clients in a fast and convenient way.

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