Proteomics Data Analysis

Simplify data; add biological meaning

Biological systems are complex, and that usually results in the design of complex experiments. Fast, powerful mass spectrometers routinely generate large data sets from proteomics analyses. A standard proteomics experiment involves not only the identification of the peptide or protein involved and its posttranslational modifications (PTMs), but also several statistical analyses that help to extrapolate the biological significance of the generated data.

Thermo Scientific offers a suite of proteomics software programs specifically designed to mine complex, high-resolution accurate-mass (HRAM) Orbitrap data, and to convert these large datasets into meaningful results.

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Simplify data extraction and interpretation

Thermo Scientific Proteome Discoverer Software offers a comprehensive set of tools for data mining of CID, HCD, ETD, and EThcD fragmentation spectra via SEQUEST, Mascot, and Byonic search engines, including mixed raw files that contain spectra from multiple fragmentation modes in a single run. The software's fast and robust algorithms enable precise peak-picking and peptide quantification for quantitative proteomics studies. Proteome Discoverer can also provide reliable statistical information, visually validate quantification results, and identify PTMs and their site locations.

Quantitate and validate peptide identity

After proteins of interest are identified in discovery experiments, their identities are verified and validated. Thermo Scientific Pinpoint Software facilitates the transition from discovery to targeted quantitation. For triple quadrupole-based selected reaction monitoring (SRM) targeted quantitation workflows, this software helps build instrument methods, process data, and generate reports. Pinpoint not only supports targeted quantitation performed by HRAM Orbitrap-based mass spectrometers; it also seamlessly integrates with Proteome Discoverer and ProteinCenter software to generate the accurate mass of isotopes or MS/MS fragment ions automatically based on the identified peptide sequence.