Identification of multiple intact proteins in a protein extract with Bioconfirm


I am using a LC-Q-TOF instrument and want to use bioconfirm to mind the masses of several proteins in a protein extract. I do not know what the proteins are, but do know the species that they come from. Should I just put the whole proteome sequence into the sequence spot in the intact protein analysis? Or is it possible to use Bioconfirm to just calculate the protein masses of each peak in the LC from the MS data?

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  • BioConfirm was not designed as a proteome search engine.  Searching for proteins using intact mass may not work since the proteome databases are based on DNA reads and include signal proteins/peptides removed from the expressed protein and the fasta file format fails to allow the inclusion of PTMs.  Protein ID is usually accomplished using MS/MS data of a protein digest and a protein database search program e.g SpectrumMill.

    Yes, you can use BioConfirm and the Maximum Entropy deconvolution algorithm to get neutral masses for each chromatographic peak.

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