New Software and Cloud-based Solutions Let Scientists Gain More Insight From Their Data
Customizable software and cloud-based tools help scientists be more productive to help accelerate metabolomic and proteomic discoveries
We are committed to the continuous development of complete and dynamic workflow solutions to further metabolomics and proteomics research


Monday, June 5, 2017 8:20 am EDT

Life science researchers can gain greater insights from their metabolomic and proteomic data and be more productive by using new software and cloud-based solutions from Thermo Fisher Scientific.

“We are committed to the continuous development of complete and dynamic workflow solutions to further metabolomics and proteomics research,” said Mark Sanders, senior director, software platform management, life sciences mass spectrometry, chromatography and mass spectrometry, Thermo Fisher. “With our comprehensive solutions, we enable our users to accelerate the pace of their research and achieve meaningful discoveries faster than ever before with the same standard of usability and performance they have come to expect from all of our systems.”

New software releases include:

  • The new Thermo Scientific Compound Discoverer 2.1 software, which supports metabolomics research insight into the biochemical phenotype of organisms. It is designed to fully utilize high-fidelity Orbitrap data for the accurate identification of compounds in the most complex matrices. The software provides customizable, fast and powerful workflows, and it combines multiple identification techniques, including fragmentation matching against the mzCloud library, which enables comprehensive small molecule characterization for scientifically relevant results.
  • Thermo Scientific Proteome Discover 2.2 software, which is designed for a range of proteomics workflows and supports multiple database search algorithms and advanced acquisition methods provided by Orbitrap mass spectrometers. The newest software release features a new XlinkX node with a fully integrated cross-linked peptide search engine, for use with the Thermo Scientific Orbitrap Fusion and Fusion Lumos Tribrid mass spectrometers, a new algorithm for label-free quantification and new tools for statistical analysis.
  • Thermo Scientific ProSightPC 4.0 software, which is ideal for researchers performing top-down and middle-down proteomics experiments. It is the recommended solution to effectively support high-mass-accuracy MS/MS experiments, enabling fast and accurate protein characterization. The software includes five search modes to help determine the exact proteoform and accommodates data acquired using a range of fragmentation techniques. The accompanying ProSightPD 1.1 Base and High Mass nodes enable automated proteoform identification within the Proteome Discoverer 2.2 framework.
  • The new Thermo Scientific Xcalibur 4.1 software, an easy-to-use, flexible and efficient solution that enables simple method setup, data acquisition, processing and reporting through an intuitive interface. Designed to integrate seamlessly with a range of Thermo Scientific LC-MS systems, the software now supports the latest Thermo Scientific Orbitrap Fusion Lumos UPVD.
  • The Thermo Scientific FreeStyle 1.3 software, which now features improved usability and offers elemental composition using MS/MS. It is a flexible data visualization solution for information rendering, rapid method development and data quality assessment.

New Cloud-based Software Applications

New cloud-based software applications, for proteomics and genomics research and applied markets, are now available through the Thermo Fisher Connect cloud-based platform. These applications include scientific data analysis and storage, remote instrument access and collaboration tools designed to help scientists accelerate their research.

  • The Sample Profiler application helps identify unknown compounds in high resolution accurate mass spectrometry sample data. It enables scientists to compare data against a database of representative compound profiles to determine trends and differences for a range of applications, including long-term monitoring of water sources for contaminant identification, adulteration of food products and identification of potential doping agents in a biological matrix.
  • The new Pathway Over-representation application helps proteomics researchers detect significant pathways within genes or proteins: Statistical analyses detect pathways that are either over- or under-represented.
  • The new Omics Comparator allows users to rapidly identify overlap and uniqueness when comparing protein or gene lists.
  • Available as both a cloud and mobile app, the new MS Instrument Connect enables researchers to monitor their LC-MS and GC-MS analyses remotely. Providing real-time updates, the app features an intuitive, at-a-glance dashboard display, detailed real-time instrument view, email notifications of sequence progress and error logs.

Thermo Fisher is featuring its new software and cloud-based applications during the 65th Annual American Society for Mass Spectrometry (ASMS) Conference, being held June 4-8, in the White River Ballroom F-J at the JW Marriott, Indianapolis. Follow these links for more information on Thermo Fisher’s dedicated portfolio of software and cloud-based applications.

About Thermo Fisher Scientific

Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of $18 billion and more than 55,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive support. For more information, please visit