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PITTCON: Software, Peptide Scoring, Search Engines


Novel and upgraded software for proteomic analysis, new peptide-scoring methods, and new ways to optimize existing search engines made a splash at this year’s PITTCON conference, held in Orlando early last month.

In a session on informatics methods used to mine mass-spectrometry data, Morgan Giddings, an assistant professor at the University of North Carolina at Chapel Hill, described her strategy for connecting genomic sequence with protein function.

Giddings acknowledged that being able to automatically translate genomic sequence into function is many years away. But in the meantime, she has developed an approach and software for analyzing mass-spectrometry data that enables mass spec data to be mapped directly to the raw genome sequence, rather than to protein sequence.

The approach, called Genome Fingerprint Scanning, allows for the identification of proteins that arise from alternatively spliced genes, proteins with mutations, and proteins with post-translational modifications.

Neil Kelleher, an assistant professor of chemistry at the University of Illinois at Urbana-Champaign, described an upgraded version of his ProSight PTM software for identifying and characterizing intact proteins and their post-translational modifications.

The upgraded program, called ProSight PC, includes five different search modes for matching top-down mass spectra with a “warehouse” of sequence that includes proteins with post-translational modifications. Thermo Electron will launch the new software at the American Society for Mass Spectrometry conference in June.

Steven Gygi, an assistant professor of cell biology at Harvard Medical School, described a way to “get a handle on” false positive protein identification rates by using a decoy database that consists of forward and reverse sequences.

If a search algorithm generates a hit in the reverse sequence part of the database, it is a known false hit, Gygi explained. He uses various methods, including adjusting search window size to keep false positive rates at one percent or less.

— Tien-Shun Lee



US Patent No. 6,864,099. Affinity selected signature peptides for protein identification and quantification.Inventor: Fred Regnier. Assignee: Purdue Research Foundation. Issued: March 8, 2005.

The patent covers a method for identifying proteins in complex mixtures that utilizes affinity selection of constituent proteolytic peptide fragments unique to a protein analyte. Mass spectrometric analysis of the proteolyzed mixture permits identification of a protein in a complex sample without purifying the protein or obtaining its composite peptide signature.


US Patent No. 6,864,089. Labeling of proteomic samples during proteolysis for quantitation and sample multiplexing. Inventors: Daniel Figeys, Matthias Mann, Ian Stewart. Assignee: MDS Proteomics. Issued: March 8, 2005

This invention relates to methods useful in the labeling of multiple polypeptide samples and subsequent analysis of these samples by mass spectrometry, particularly in the high-throughput proteomic setting. The method involves differential isotopic labeling of peptide or protein samples in order to identify the source of the sample, to permit multiplexing of samples during the sequencing step by mass spectroscopy, or to perform sample relative quantitation of proteins differently expressed in biological samples.




In March, the Protein Structure Initiative reported that it had determined the structures of more than 1,000 different proteins. PSI is a 10-year, approximately $600 million project funded largely by the National Institute of General Medical Sciences.


NHLBI has awarded Insilicos a two-year, $400,000 grant to develop a general-purpose proteomics software suite based on the Institute for Systems Biology’s Trans-Proteomic Pipeline software.


Geneva Bioinformatics has incorporated the mzData open-source format — devised by HUPO’s Proteomics Standards initiative — into the latest version of its Phenyx protein-identification software.


Also, Geneva Bioinformatics and the Current Science Group, a London-based publishing concern, have formed a joint venture. The new company, called Current BioData, will develop, promote, and distribute ProXenter, a Web-based protein database product developed by GeneBio over the last three years.


Applied Biosystems and MDS Sciex will work with Biocrates Life Sciences of Innsbruck, Austria, to develop methods and consumables for metabolomics experiments using the ABI/MDS Sciex QSTAR LC-MS/MS and API 4000 Q-LC-MS/MS.


Lumera will collaborate with the Institute for Systems Biology to develop a label-free protein microarray platform that will include Lumera’s NanoCapture microarrays and its ProteomicProcessor reader. The new system will enable researchers to perform real-time kinetic measurements of protein-protein, protein-drug, and protein-DNA interactions.


The Scan

Support for Moderna Booster

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Testing at UK Lab Suspended

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J&J CSO to Step Down

The Wall Street Journal reports that Paul Stoffels will be stepping down as chief scientific officer at Johnson & Johnson by the end of the year.

Science Papers Present Proteo-Genomic Map of Human Health, Brain Tumor Target, Tool to Infer CNVs

In Science this week: gene-protein-disease map, epigenomic and transcriptomic approach highlights potential therapeutic target for gliomas, and more