1 / 6

Generalized Protein Parsimony

Generalized Protein Parsimony. Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center. Traditional Protein Parsimony. Select the smallest set of proteins that cover all identified peptides . Sensible principle, implies

kylar
Télécharger la présentation

Generalized Protein Parsimony

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Generalized Protein Parsimony Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center

  2. Traditional Protein Parsimony • Select the smallest set of proteins that cover all identified peptides. • Sensible principle, implies • Eliminate equivalent/subset proteins • Unique peptides force proteins into solution • Bad consequences for FDR filtered ids • Impact most tools, even probability based ones

  3. Must ignore some PSMs • Improving peptide identification sensitivitymakes things worse! • False PSMs don't cluster PSMs PSMs 2x Proteins 10%

  4. Must ignore some PSMs • A single additionalpeptideshould not force proteins into the solution

  5. Generalized Protein Parsimony • Weight peptides by number of PSMs • Constrainunique peptides per protein • Maximize covered peptides (PSMs) • Can match filtering FDR to uncovered PSMs • Readily solved by branch-and-bound • Reduces to traditional protein parsimony

  6. Match FDR to uncovered PSMs Traditional Parsimony at 1% FDR: 1085 (609 2+-Unique) Proteins

More Related