Identification of multiple intact proteins in a protein extract with Bioconfirm

To follow up on this, I tried putting in the fasta of the whole proteome into the sequence manager (which took a very long time as it was a large fasta file), and now when I try to select sequences it is really slow and the software stops responding. Any advice would be appreciated.

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.

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.