Thermo Fisher Scientific has upgraded five software packages targeted at qualitative and quantitative proteomics.
Proteome Discoverer analyzes qualitative and quantitative proteomics data via a workflow-driven graphical user interface. New features include support for a "wide range" of SILAC experiments and enhanced capabilities for relative quantitation using isobaric mass tags, such as Tandem Mass Tags.
ProteinCenter is a web-based tool for integrating, interpreting, and sharing proteomics data. It links peptide-centric information from Proteome Discoverer with content in public data repositories such as UniProt. ProteinCenter currently contains more than 13 million unique protein sequences, Thermo said.
Sieve is an automated solution for label-free, semi-quantitative differential expression analysis of proteins, peptides, and metabolites. It now includes a machine-learning algorithm to compute false discovery rates, as well as receiver operating characteristic analysis, which "offers a powerful way to discriminate between disease and normal protein classes," the company said. The software also now offers sample concentration normalization in order to automatically adjust the expression ratios of differential analysis results.
Pinpoint allows researchers to use previously acquired discovery data to help develop quantitative biomarker validation assays for the company's TSQ triple-stage quadrupole instruments. New features include retention time modeling to simplify reproducibility assessments and minimize run-to-run variability. The software also includes new peptide-screening algorithms.
ProSightPC is used to identify and characterize peptides and intact proteins and is "complementary" to Proteome Discover, the company said. ProSightPC processes MS/MS data, including proteins with known sequence variants and post-translational modifications, and also takes into account prior biological knowledge in its database search. The software also offers a flexible search mode that can be used to identify unknown or unexpected modifications, Thermo said.