Are Your LC-MS/MS Experiments Reproducible?

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

Hint of the day: We are offering a 30-day free trial! Click here to get started...

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MassQC Release Notes...

Why MassQC?

Leading researchers suggest that rigorous, quantitative assessment of system performance is essential to Proteomics' success. More replicates, better upstream preparatory methods, and a more thorough Quality Control protocol are among topics discussed as areas for improvement. Proteome Software and others (see the Fixing Proteomics Campaign for more info) have confirmed this need. The solution? MassQC: a simple-to-use, very affordable web-based application that helps researchers accomplish better LC-MS/MS reproducibility.

What is MassQC?

MassQC is an online Quality Control tool that helps you achieve more reproducible LC-MS/MS experiments, while reducing time spent assessing the performance of your instrumentation. MassQC improves reproducibility by examining repeated, standard runs for a small number of known proteins, and covers both width and breadth of your LC-MS system performance. Chromatorgaphy (peak widths and retention time spread), Ion Source (spray instability and charge distribution), Dynamic Sampling (trigger point and oversampling), and Identifications (mass accuracy and number of peptides identified) are among the 28 metrics MassQC analyses.

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:

By helping you discover performance problems early, MassQC saves valuable time and prevents wasting precious, difficult-to-obtain patient samples. Single-click uploads of Thermo Orbitrap or LTQ Data Dependent *.raw MS/MS files make it simple to begin tracking LC-MS system performance. This allows you to tune your instrument and identify more proteins and helps the technician identify maintenance needs before they become a problem.

Using MassQC is inexpensive: $100/month per instrument ($60/month per instrument for academic labs)

Using MassQC is cost effective: save time and money by finding common problems such as poor chromatography (caused, for example, by degrading columns) and decreasing sensitivity and ion intensity (from dirty ion optics).

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

In other news. . .

Scaffold 2.6.01 was recently released and 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), and Waters IdentityE (*.xml, using Scaffold Plug-in from the PLGS).

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