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Thermo Fisher Scientific introduced a suite of five complementary software products for qualitative and quantitative proteomics at the Human Proteome Organization (HUPO) 2010 Congress.

Working in concert with Thermo Scientific mass spectrometers, the software solutions provide researchers with fast and simple workflows for persistent proteomics research challenges.

These solutions are intended to drive progress in key industry initiatives such as the Human Proteome Project launched at the HUPO 2010 conference.

Andreas Huhmer, proteomics marketing director for life sciences mass spectrometry at Thermo Fisher Scientific, said: ‘The software innovations presented at HUPO strengthen our industry-leading workflows for qualitative and quantitative proteomics.

‘This unique suite of software complements the power of Thermo Scientific mass spectrometry, sample preparation and chromatography technologies to facilitate researchers’ success in proteomics applications.

‘This covers everything from comprehensive protein identification and phosphoprotein characterisation, relative protein quantitation and the targeted validation of biomarker candidates,’ added Huhmer.

The new Thermo Scientific Proteincenter software is a web-based tool designed to provide the faster integration, interpretation and sharing of proteomics data.

It links peptide-centric information derived from the Thermo Scientific Proteome Discoverer software with the protein-centric content of biological data repositories such as the Uniprot and NCBI databases, enabling users to compare and interpret data in minutes.

The Proteincenter software now contains more than 13 million unique protein sequences and accesses, updates and integrates publicly available protein information on a biweekly basis.

The Proteome Discoverer software is ideal for the analysis of qualitative and quantitative proteomics data.

It addresses the need for flexibility by offering a range of bio-software tools and customisable workflows for a range of proteomics experiments in a workflow-driven graphical user interface.

The software is optimised to take advantage of the high-resolution data and multiple complementary fragmentation methods offered by Thermo Scientific mass spectrometers.

The Proteome Discoverer software can boost productivity and improve quantitative results.

It now supports a range of stable isotope labelling with amino acids in cell culture (SILAC) experiments to accelerate the quantitation of protein expression levels from differentially treated cell populations.

This simplifies the analysis of complex SILAC experimental data.

It also offers enhanced capabilities for relative quantitation using isobaric mass tags, such as Thermo Scientific Tandem Mass Tags (TMTs), with the statistical analysis of results.

The flexible handling of peptide identification improves coverage and relative quantitation, and data processing following data collection can now be automated.

The Thermo Scientific Sieve software is an automated solution for the label-free, semi-quantitative differential expression analysis of proteins, peptides and metabolites.

Using the Sieve software to pre-filter data reduces the number of components that need to be identified, which should increase the throughput of complex biomarker discovery experiments.

The Sieve software offers improved confidence in protein identifications with the addition of a machine-learning algorithm to compute false discovery rates.

The inclusion of a statistical analysis capability, receiver operating characteristic (ROC) analysis, offers a method for discriminating between disease and normal protein classes and helps to classify the relevance of single and multiple biomarker candidates.

The software now provides sample concentration normalisation to automatically adjust the expression ratios of differential analysis results.

Complete integration with the Proteome Discover software enables users to apply protein-search identification capabilities to their differential analysis results.

The Thermo Scientific Pinpoint software simplifies the transition from early-stage biomarker discovery to the larger-scale, quantitative verification of putative biomarkers.

It allows researchers to leverage previously acquired discovery data to accelerate and simplify the development of quantitative assays for all experimental approaches using intelligent SRM (iSRM).

According to the company, iSRM – available on Thermo Scientific TSQ triple-stage quadrupole instruments – is designed to increase the sensitivity, selectivity and throughput of targeted quantitation assays, allowing the simultaneous verification and quantification of thousands of targeted peptides in a single run.

The Pinpoint software now offers retention time modelling to simplify reproducibility assessments, to minimise run-to-run variability and to increase confidence in results.

New peptide screening algorithms enhance the identification of peptide candidates.

Finally, the Thermo Scientific ProsightPC software harnesses the high precursor and fragment mass accuracy of Thermo Scientific mass spectrometers to provide the accurate identification and characterisation of peptides and intact proteins.

Complementary to the Proteome Discover software, ProsightPC processes accurate-mass MS/MS data, whether from top-down or bottom-up experiments, including proteins with known sequence variants and post-translational modifications (PTMs).

It also takes into account prior biological knowledge in its database search.

The software offers a flexible search mode that can be used to identify unknown or unexpected modifications.

Leveraging high mass accuracy, ProsightPC can reduce the complexity of multiplexed fragmentation to make multiple identifications from a single MS/MS experiment.

Thermo Fisher Scientific (Mass Spectrometry)

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