Bioproximity New Release: Proteome Cluster

Jan. 3, 2012 - PRLog -- Search Parameter Imports

Users have always been able to export the XML-based search parameters used for any search. Now you may import those search parameter files. This permits easy sharing of search parameters with colleagues down the hall or around the world. No longer do you have to wonder if the different search results you are seeing are the result of a data entry error.

Sequence-Based Refinement

One of the more powerful features of X!Tandem is the sophisyicated refinement module. A refinement search follows a standard search and only searches proteins which were found in the original search. But it is not just the same search repeated, that wouldn't be very useful, the refinement search allows you to specify specific post-translation modifications, non-specific cleavage products, point mutations and peptides to those proteins discovered by previous GPM users.

It is useful for maximizing sequence coverage and discovering properties of the protein which might otherwise go undetected. For example, peptides sometimes fragment during the ionization process, leaving a "semi-tryptic" peptide which would not be picked up in a standard search requiring tryptic cleavage sites at both ends of the peptide.

A refinement search can identify these peptides. It is much more efficient to search for such peptides in a refinement search, when most of the detectable proteins present have been identified, rather than in the initial search.

A "semi-tryptic" search run at the outset will take far longer than a search requiring strict tryptic specificty because of the larger search space and will assign lower expectation values to identified peptides, also due to the increased search space.


Full release on the site:  http://www.bioproximity.com/

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Bioproximity, LLC
7001 Loisdale Rd. Suite C, Springfield, VA 22150, USA

Bioproximity is a contract research organization specializing in biological mass spectrometry for protein analysis and proteomic informatics. We offer a wide range of proteomics services customized to the needs of our clients. Combining state-of-the-art instrumentation, methods and informatics we provide unparalleled sensitivity and throughput for your application.

Bioproximity, LLC offer:
* Biologic and biosimilar characterization
* Bioprocessing pipeline optimization and quality control
* Host-cell protein profiling for CHO and other organisms
* Biomarker discovery via global or targeted proteomic profiling
* Protein identification
* Post-translational modification enrichment and/or characterization
* Characterization of immunoprecipitated proteins and complexes