November 9th, 2010, 11:30 am
My work, and links to my tools, have been featured in the clinical proteomics technology initiative (CPTI) eProtein newsletter, “Researcher Spotlight: Enabling the Search for Novel Cancer Protein Variants.” Check it out, and give the Peptide Sequence Database (PepSeqDB), Peptide Arbiter by Machine Learning (PepArML) Meta-Search Engine, and PeptideMapper tools a try.
The PepSeqDB fasta sequence databases provide a comprehensive enumeration of (putative) peptide sequences from ESTs, mRNAs, and protein sequence databases for human, mouse, rat, and zebra-fish.
The PepArML meta-search engine searches tandem mass-spectra against protein sequence databases (including PepSeqDB) using seven search engines (Mascot, Tandem, Tandem with K-Score and S-Score scoring plugins, OMSSA, Myrimatch, and InsPecT) and combines the search results using unsupervised machine-learning. This infrastructure typically identifies two-to-three times more spectra than individual search engines at 10% FDR.
The PeptideMapper web-service provides real-time, one-click mapping of peptide sequences for human, mouse, or rat, to a genome annotation track of the UCSC genome browser, and onto their protein, mRNA, and genomic evidence. Peptides containing (coding) single nucleotide polymorphisms (SNPs) at also mapped, making it possible to evaluate cSNPs by their mass-delta, amino-acid substitution, and genomic context.
October 6th, 2009, 9:17 am
Meeting program is here for future reference. My talk and poster are available on the Edwards Lab publications page.
September 21st, 2009, 3:31 pm
I gave a talk in the NIH Proteomics Interest Group seminar series on Friday (9/18).
Improved Peptide Identification Sensitivity using Meta-Search, Grid-Computing, and Machine-Learning, with Application to Genome Annotation
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October 30th, 2008, 1:08 pm
A fun couple of days. Unfortunately, I missed David Altschuler’s talk because I left my poster in D.C. and had to get it re-printed at the local Kinko’s and pinned-up before 10am. Meeting program is here for future reference. Highlights for me were the talks by Alexey Nesvizhskii on some statistical properties of spectrum counting, David Tabb on the DirecTag MS/MS search by sequence tag software, D. R. Mani on the PEPPeR label-free LC/MS quantitation software, and Dick Smith talking about cool new mass-spec tech (IMS), his comments on the bleary future of ion-traps, and the promise of high-accuracy TOF-TOF instruments – it was fun to chat with Marvin Vestal, and later hear his comments on Dick’s talk – something about the rest of the world finally coming around to his point of view :-). My talk and poster are available on the Edwards Lab publications page.
September 19th, 2008, 11:26 am
Just been notified that my abstract has been accepted for an oral presentation at the Clinical Proteomics Technologies for Cancer 2008 Annual Meeting in Boston, October 28 & 29. The CPTC is the NCI initiative which supports my R01 grant “Proteomics characterization of alternative splicing and cSNP protein isoforms” under the Advanced Proteomic Platforms and Computational Sciences program. I’ll be presenting on Tuesday October 28, 1:55-2:20.
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