Thermo Fisher Scientific Announces Enhancements to its Quantitative and Qualitative Proteomics Tools at ASMS 2010

Thermo Fisher Scientific Inc. announces important enhancements for its proteomics tools that promise to facilitate breakthrough progress in quantitative and qualitative proteomics. The new products work in concert with other Thermo Fisher Scientific products including reagents and consumables to create simpler, time-saving workflows. These solutions were be displayed at the ASMS Conference on Mass Spectrometry and Allied Topics in Salt Lake City, Utah.

“Breakthrough discoveries in biology and progress in biomarker research have been made possible in large part by new technologies. The Thermo Scientific brand is a leader in such innovative technologies, and provides a full line of products that integrate seamlessly into solutions. These include mass spectrometry and liquid chromatography systems, software, and sample preparation reagents and kits,” said Andreas Huhmer, proteomics marketing director for life sciences mass spectrometry at Thermo Fisher Scientific. “The products we showcase at ASMS strengthen our ability to provide researchers with end-to-end solutions that reduce complexity and increase the speed of, and information derived from, proteomics workflows.”

Pinpoint software enhances productivity and confidence in results
Thermo Scientific Pinpoint software simplifies the transition from early-stage biomarker discovery to larger-scale, quantitative verification of putative biomarkers. It allows researchers to leverage previously acquired discovery data from mass spectrometers such as the Thermo Scientific LTQ Velos and LTQ Orbitrap Velos to speed and simplify development of quantitative assays using intelligent SRM (iSRM). One of the biggest challenges in quantitative proteomics is to simultaneously verify and quantify low-level biomarkers reproducibly from run-to-run. iSRM, available on all Thermo Scientific TSQ triple-stage quadrupole instruments, increases the sensitivity, selectivity, and throughput of targeted quantitation assays allowing the simultaneous verification and quantification of thousands of targeted peptides in a single run.

A prototype version of Pinpoint™ software was distributed to over 300 proteomics researchers worldwide who used it to increase productivity and further proteomics research. Thermo Fisher Scientific incorporated their feedback into a commercially available version, with enhancements that are designed to optimize productivity, data quality and confidence in results. The software now processes a large number of data files, enables researchers to incorporate information from global protein and peptide spectral databases, and has been enhanced to facilitate analysis of phosphopeptides and glycopeptides.

Proteome Discoverer software enhances productivity and quantitative results
Thermo Scientific Proteome Discoverer software is a comprehensive platform for the analysis of quantitative and qualitative proteomics data. It addresses the need for flexibility by offering a wide array of bio-software tools and customizable workflows for every imaginable proteomics experiment.

Proteome DiscovererTM software has new capabilities that boost productivity and improve quantitative results. It now supports a wide range of stable isotope labeling with amino acids in cell culture (SILAC) experiments to speed quantitation of protein expression levels from differentially treated cell populations. SILAC experiments that were once very tedious are now remarkably easy. It also offers enhanced capabilities for relative quantitation using isobaric mass tags, such as Thermo Scientific Mass Tags (TMT), with statistical analysis of results. Flexible handling of peptide identification improves coverage and relative quantitation, and data processing following data collection can now be automated.

EASY-nLC II nano-LC boosts performance and productivity
The Thermo Scientific EASY-nLC II system represents a breakthrough in nano-LC technology. It uses a split-free design to achieve stability and reproducibility. Unlike other nano-LCs, it is designed exclusively for proteomics and provides nanoflow performance right out of the box. It is easily coupled with the powerful Thermo Scientific ion trap, hybrid and triple quadrupole mass spectrometers. Its predecessor, the EASY-nLCTM, has been adopted by the world’s leading proteomics research centers for its exceptional simplicity, performance and ease of use.

The EASY-nLC II features an intuitive graphical user interface, touch-screen operation and remote diagnostics capability. It is compact, and includes an autosampler that provides reproducible low-nanoliter injections. The EASY-nLC II includes new features designed to boost performance and productivity, including support for unattended analysis of 384-well plates; an integrated, refrigerated autosampler for improved sample stability; and intelligent flow control to speed equilibration and sample loading. The EASY-nLC II provides two-dimensional chromatographic capability to identify more proteins than conventional methods, without the increased complexity of added valves and pumps.

New Cysteine-Reactive Tandem Mass Tag (cysTMT) Reagents and Fe-NTA Phosphopeptide Enrichment Kit save time and improve protein identifications
Isobaric mass tags such as the Thermo Scientific Tandem Mass Tag Reagents enable concurrent identification and multiplexed relative quantitation of multiple protein samples using tandem mass spectrometry. The new Thermo Scientific cysteine-reactive tandem mass tag (cysTMT) reagents can be used to perform two-plex or six-plex quantitation of cysteine-containing peptides. To selectively analyze the cysteine-labeled peptides, the sample is enriched using the Thermo Scientific immobilized anti-TMT antibody resin. Together, the cysTMTTM reagent and immobilized anti-TMT antibody resin reduce sample complexity and improve dynamic range, making it possible to identify a unique set of proteins.

The new Thermo Scientific Pierce Fe-NTA Phosphopeptide Enrichment Kit allows fast, efficient enrichment of phosphorylated peptides. Its spin columns are easy to use and can parallel process multiple protein digests in less than 30 minutes for analysis by mass spectrometry. High-binding capacity resin allows enrichment of up to 150 micrograms of phosphopeptides per column. The kit contains detailed instructions and all necessary components to load, wash and elute phosphopeptides. It is compatible with samples digested in solution or after in-gel digestion.