Introducing SEQUEST 3G - A New Translational Proteomics Standard

What exactly is SEQUEST 3G? What can it do for me?
SEQUEST 3G is the latest, next-generation SEQUEST standard specifically developed and optimized for translational proteomic applications involving phosphorylation and other post-translational modifications (PTMs). Defined by Sage-N Research in close collaboration with Dr. John R. Yates, III of the Scripps Research Institute, SEQUEST 3G defines a single common standard for similarity scores, search parameters and statistics, and input/output file formats and is ideal for noisy and poor quality spectra. This robust proteomics search engine maintains compatibility with existing TPP and Scaffold workflows, and incorporates new features of the latest technologies such as electron-transfer dissociation (ETD) and high mass accuracy instruments. SEQUEST 3G also supports multiple scoring and rescoring algorithms such as ASCORE. In addition to improved sensitivity identification for phosphopeptides and low-abundance spectra, the SEQUEST 3G is a significant update that enables future complex functionality and addresses prior version incompatibilities and calculation variances.

How do I obtain SEQUEST 3G?
SEQUEST 3G is being released as an embedded component within the SORCERER v4.0 platform being released in Q1 of 2010. Whereas earlier versions (such as SORCERER-SEQUEST) relied upon a single pass, the new v4.0 platform uses a more efficient “multiple-pass” search engine architecture involving a first-pass with SEQUEST 3G to keep the top 50 candidates and then subsequent rescoring passes with other search engine modules. Current customers will receive an automatic Q1 update as part of their standard maintenance package. This update is conveniently backward-compatible in two ways: the subsequent pass is optional, and can be combined with other rescoring functions in a MUSE scripting environment.

SEQUEST 3G is available for licensing within third-party bioinformatics software suites for a variety of mass spectrometers and technologies. A SEQUEST 3G press release can be found atwww.sagenresearch.com/news_11.html

Which SORCERER is right for you?

As you may know, Sage-N Research offers three SORCERER platforms — the SORCERER Enterprise, the SORCERER 2, and the SORCERER Lab.

The SORCERER Enterprise
The SORCERER Enterprise is a customizable and secure throughput and biorepository system for aggregate analysis. Provided as a scalable Blade server with integrated life-science optimized storage, the Enterprise system handles up to a few terrabytes of data and is highly scalable using additional computing resources. This platform is ideal for labs that are highly productive or focused on generating continuous high-throughput data, and can analyze 100,000+ spectra/hour — even those with post-translational modifications.

The SORCERER 2
The SORCERER 2 is a mainstream product for most proteomic labs — those with frequent but not continuous high-throughput needs. It is well-suited for modern instruments like the Thermo LTQ and Orbitrap, ABI 4700 and 4800, and Waters SYNAPT G2 and handles 2+ MS spectra/second, or 30,000+ spectra/hour. This system is a stand-alone platform and not scalable like the SORCERER Enterprise.

The SORCERER Lab
The SORCERER Lab is a lower-cost, entry system that is simple, lightweight, and compact. Designed to plug-and-play and require low IT maintenance, it contains the most essential yet basic capabilities, including SEQUEST 3G, TPP, and Scaffold. The SORCERER Lab is still more powerful compared to other PC-based systems. At 10,000+ spectra/hour, it has one-third the analytical throughput of the Discovery system.

What application is each system ideal for?
The SORCERER Enterprise and SORCERER 2 systems are appropriate for serious labs with large demands. Both can embed third-party Linux and Windows applications. Furthermore, theSORCERER Enterprise is best-suited for large pharma or high-throughput proteomics labs, while the SORCERER 2 is ideal for mainstream core facilities and medical schools and industry labs or groups with occasional needs. The SORCERER Lab is an entry-level system appropriate for smaller groups with less demand, such as 3-4 individual researchers.

I’m still not sure which system is best for my needs. Where do I find answers?
This is a cursory overview to introduce our three SORCERER systems. For an evaluation, please contact our Informatics Specialist Mark Pitman by email or at (408) 841-7185 ext. 39. Based on your current (and if relevant, future) throughput, lab profile, research, and workflows, we will provide a recommendation for a platform and customizations.

This month’s scoop: Protein Pipeline Identification Using SORCERER 2 and SEQUEST
Deborah H. Lundgrena^a, Harryl Martinezb^b, Michael E. Wrightb^b, David K. Hana^a
aDepartment of Cell Biology, Center for Vascular Biology, University of Connecticut Health Center, Farmington, Connecticut
^bDepartment of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, Iowa

Current Protocols in Bioinformatics
Unit Number: UNIT 13.3.1-13.3.20
DOI: 10.1002/0471250953.bi1303s28
Print Publication Date: December, 2009
John Wiley & Sons, Inc.

Dr. Wright’s group in the Department of Molecular Physiology and Biophysics at the University of Iowa focuses on using state-of-the art quantitative MS to study protein complexes in higher organisms.

Dr. Han and his team at the University of Connecticut are interested in the control of signalling pathways by protein complexes, and utilize both classic protein fractionation techniques as well as newer nano-electrospray LC tandem MS.

These two groups have collaborated on this comprehensive publication that walks through the basic steps of processing MS data with Sorcerer 2 and SEQUEST and analyzing results using TPP and Scaffold. In addition to providing a helpful overview of the SEQUEST algorithm, this Current Protocols tutorial article details relevant SORCERER-SEQUEST enhancements and discusses data filtering methods.

There are many relevant, helpful explanations and notations to help orient users to screens, fields, and commands that are of significant or particular interest. Especially useful are concise yet thorough links summaries (and locations) for key screens and displays along the step-by-step process. A highlight is the considerable detail regarding the different format and output criteria and options available to the user, as well as critical assessments of which one is most appropriate for what situation. This tutorial is anchored by author insights and recommendations for data analysis and interpretation. The co-authors have clearly spent the time and effort to use, explore, and understand the capabilities and functionality of SORCERER 2 and SEQUEST.