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  • CPTI eProtein Newsletter Researcher Spotlight feature

    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.

     

     


    CPTC 2009 Annual Meeting

    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.


    NIH Proteomics Interest Group Talk

    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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    PepArML Meta-Search Engine

    June 1st, 2009, 12:01 pm

    The PepArML meta-search engine is open-for-business. New users can register for free, upload their spectra, submit large-scale meta-searches, monitor the search jobs, combine the completed searches using PepArML, and download the results, all via on-line PepArML meta-search engine site.

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    Mapping peptides to the UCSC genome browser

    February 17th, 2009, 5:26 pm

    Announcing new features provided by the PeptideMapper service from the Edwards Lab.

    The PeptideMapper Web-Service already provides real-time peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb from human, mouse, rat, and zebra-fish. Results can viewed interactively or retrieved using HTTP or SOAP requests.

    Now, the PeptideMapper Web-Service supports real-time mapping of peptide sequences to the UCSC genome assemblies via the UCSC’s so-called “known genes” – enabling “one-click” display of peptide sequences in the UCSC genome browser. Projecting peptide sequences into the UCSC genome browser aids in the interpretation of the genomic evidence in support of peptides identified directly from proteins, by tandem mass spectrometry.

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    PeptideMapper Web-Service

    November 24th, 2008, 4:54 pm

    Announcing a new service, PeptideMapper, from the Edwards Lab.

    The PeptideMapper Web-Service provides peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence.

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