Welcome to the Proteome Software Newsletter !

>>> Release Notes

As many of you remember from our last newsletter, we have a new Quality Control tool, MassQC.

Hint of the day: Sign up for a free 30-day trial of MassQC. Click here for more details...

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Why MassQC?

There has recently been a push for an improvement in the way the Proteomics Community collects and handles LC-MS/MS data. More replicates, better upstream preparatory methods, more thorough Quality Control protocols have all been discussed as areas for improvement. Proteome Software and others (see the Fixing Proteomics Campaign for more info) have seen this need and developed tools to address the solutions.


What is MassQC?

MassQC is an online service for Proteomics that analyzes, displays, and compares standard LC-MS/MS runs. Based on Performance Metrics developed by the National Institute for Standards and Technology (NIST), MassQC was developed to assist researchers in comparing their historial QC data to the current performance of their LC-MS/MS instrumentation. To learn more about the origins of these metrics, see the NIST publication.


About MassQC:

Preparation may take days. Each sample can represent an investment of thousands of dollars. It's only logical to increase confidence in the instrument by using MassQC. It's a simple process: run a standard protein mix such as BSA, upload the Thermo *.raw Data Dependent MS/MS files to MassQC with a click, then compare the latest result to your growing historical record. This reduces wasted time and samples, allows you to tune your instrument and identify more proteins and helps the technician identify maintenance needs.

MassQC uses the following process to analyses your standard QC samples: first the *.raw file is uploaded to the MassQC servers; next, ReAdW examines the chromatographic peaks and converts the file to *.mgf; and then the search engine, either OMSSA for simple standards or SpectraST for complex standards, reads this file and searches the database for peptide IDs; finally, MassQC computes the Metric values and diplays them in MassQC.

If you would like to give MassQC a try, please click the following link.


In other news. . .

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), Discoverer (*.msf, xscore), and Waters IdentityE (*.xml, using Scaffold Plug-in from the PLGS). And coming soon... Discoverer (*.msf Z-Score).

If you have any questions about Proteome Software, Scaffold/Scaffold Q+ or MassQC, contact us here.

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Proteome Software, Inc
1340 SW Bertha Blvd, Suite 10
Portland, OR 97219
Toll-Free (800) 944-6027