Sequest, by Thermo Sciences, is a search engine that matches tandem mass spectra with peptide sequences. CPAS uses Sequest to search an mzXML file against a FASTA database and displays the results in the MS2 viewer for analysis. The Sequest executable from BioworksBrowser 3.2 and 3.3 was used to create this integration. CPAS connects to a Sequest search engine via a web application installed on the Sequest server. The web application, SequestQueue, is part of the CPAS project, see Downloading and Installing the SequestQueue Web Application.  It must be installed on the same computer as Sequest or on the master node of a Sequest Cluster.  To activate Sequest searches from CPAS the URL of the Sequest server is entered on the CPAS installation’s site configuration page, see Customizing the Site. When CPAS is configured to use Sequest, Sequest will appear as an additional search engine choice when performing searches.

Because CPAS can search with several different search engines, a common format was chosen for entering search parameters. The format for the search parameters is based on the input.xml format, developed  for X!Tandem. The CPAS installation includes a set of default Sequest search parameters. These default parameters can be overwritten on the search form.

A search submitted to the SequestQueue from the CPAS server will go through the following steps:

1. The input.xml parameters are translated to a sequest.params file.
2. The sequest.params and MzXML files are downloaded to the Sequest server via the SequestQueue.
3. The SequestQueue will create a job request and place it in a queue.
4. When the job request reaches the front of the queue the MzXML file will be parsed into Sequest DTA files using MzXML2Search.exe.
5. Sequest analyzes the .dta files to produce .out files.
6. The .out files are converted to a summary.html file with Out2Summary.
7. The CPAS install uploads the summary.html, converts it to pepXML, and continues processing.

The Sequest/CPAS integration was made possible by: