Welcome to the Proteome Software newsletter

This marks our first delivery of what we hope to be an informational and educational newsletter about Proteomics/Bioinformatics and some of the software tools we offer to assist you in deciphering this complex field

Hint of the day: You can create reverse FASTA databases inside Scaffold. To Learn how, click here

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MassQC, scheduled for release on October 1st, 2009 is an online service that stores, analyzes and displays performance metrics for LC-MS/MS proteomics. It simplifies and speeds up the process of quality control. Sign on to MassQC, and you can discover variation early, before you waste valuable samples and time. For more information, visit: the massQC website

The Bioinformatics Core at University of Pittsburg have produced some great results highlighting the importance of correct identification of peptides and proteins in complex mixtures. As most of you know this can be a daunting task, especially without the correct software tools. Here's the paper

Proteome Software launched its quantitative module, Scaffold Q+, at ASMS 2009. This tool allows for visualization of protein abundances across multiple iTRAQ and TMT experiments. You can filter and sort differentially expressed proteins, as well as track the individual peptide levels in your samples. For more information, visit the Proteome Software Scaffold Q+ website

In other news. . .

Scaffold currently allows you to download the GOA database to your local computer and query your proteins quickly for GO terms. Earlier this year, NCBI changed their format for their GO database, so this function was disabled in Scaffold. We have made the necessary fixes and this feature is now available again

Many of our users process a large number of search results using our batch processing version of Scaffold. ScaffoldBatch is run from the command line and can process simultaneous jobs be hind the scenes. For more information about batch, contact us here

Scaffold reads the following files: Mascot (*.dat), Sequest (*.srf, *.dta/*.out, *.ms2/*.sqt), X! Tandem (*.xml), Phenyx (*.scaffold-pidres.xml), Spectrum Mill (each search result is a directory of files-load the whole directory), OMMSA (*.omx), and Discoverer (*.msf, xscore), and Waters IdentityE (*.xml, using Scaffold Plug-in from the PLGS). And coming soon... Discoverer (*.msf Z-Score)

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Proteome Software, Inc
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