Manually verifying peptide identifications

If you depend on a computer to identify proteins, it's important to verify that the system is working correctly. Automatic identifications provided by SEQUEST or Mascot, and even those further refined by Scaffold, may need to be manually verified for critical or questionable results. Doing this manual verification requires a in-depth understanding of peptide spectra. »More

Interpreting MS/MS Proteomics Results

Join Brian Searle on an illustrated tour about interpreting MS/MS peptide spectra. On this tour you will first see how you can relate mass spectra to peptides. Next you see why the SEQUEST software was developed to interpret these spectra as peptides. Next you will see other software approaches have been developed and how combining approaches produces even better results.»More

Proteomics Forum

Proteome Software would like to hear what you have to say about Proteomics, and to encourage discussion between professionals. What do you believe are the most important issues facing the discipline? What challenges you in your daily work? What tools would you love to work with -- if only they existed?

To get the discussion started, Proteome has established a forum for discussion of proteomics and software. It's built in a WIKI format to make it easy for you to add your own views and comment on ours.

We've inaugurated the forum with an essay called "Question Assumptions". It's designed to encourage your inner skeptic by questioning the hidden assumptions that software makes about the data it processes. Take a look and add your comments. »More

Posters

Posters that Proteome Software and collaborators have presented at ASMS, ABRF and HUPO. These posters are about protein identification, Scaffold and related work. »More

Combining Multiple MS/MS Searches For Increased Peptide Identification

SEQUEST matches MS/MS spectra and peptides. So does Mascot. So does X!Tandem. Each of these search engines only matches fraction, usually less than 20 or 30 percent, of the spectra. Typically other spectra are discarded. One way that we can dig deeper to find information in these discarded spectra is to combine SEQUEST's matches with X!Tandem's. Or Mascot's with X!Tandem. Or SEQUEST with Mascot. Two searches dig up more information than one. »More

Explaining PeptideProphet

When using SEQUEST, what represents a good score? When using Mascot, what is the trade-off of missed identifications to false positives? These are hard questions whose answers depend on the instrument, sample complexity, FASTA database size, and experimental design. The PeptideProphet algorithm gives the answers. »More

Explaining X!Tandem

X!Tandem is a protein search engine available from The Global Proteome Machine Organization that runs much faster than other free search engines. X!Tandem is open source software that automatically searches for missed cleavages, semi-tryptic peptides, post-translational modifications, and point mutations. »More