Discovering relevant protein biomarkers

Proteins and related molecules are frequently the focus of translational research. They have great potential as both diagnostic markers and therapies. Translational proteomics most frequently involves the discovery of potential clinically relevant protein biomarkers and moving as quickly as possible from positive identification to verification and validation of the protein(s) as markers. Research into protein pathways, characterization of post-translational modifications, protein expression profiling, and proteoform characterization are also common aspects of translational research. Thermo Fisher Scientific is the worldwide leader in liquid chromatograph mass spectrometer solutions for protein research. Our sample preparation technologies, instrument systems, and data analysis software are advancing that limits of proteomics knowledge.

Featured videos

Dr. Steven Gygi of Harvard University Medical School describes the power of multiplexed proteomics and his new Center for Multiplexed Proteomics.

Dr. Kathryn Lilley of Cambridge University discusses the cellular locations of proteins and how advances in mass spectrometry and mass tagging provide a more complete picture of protein distribution and function.;

Proteomics: from discovery to routine

The earliest stages of translational research involves the discovery of putative biomarkers, which requires instruments and workflow methods that can resolve huge numbers of analytes and provide relative differential quantitation to be able to identify proteins and other compounds of interest.  As the research progresses to biomarker confirmation, assay development and validation work, the number of analytes of interest is dramatically narrowed, while the need for highly sensitive quantitation and sample throughput become the most important issues.

  1. Discovery - Sample identification, characterization, definition of a candidate target list, biological interpretation
  2. Verification - Targeted quantification of candidate (subset of previously detected analytes) targets, generating verification data
  3. Validation - Targeted quantification of “verified” candidates in greater number of samples to account for biological variation

Move into next phase - assays are developed for routine detection


Featured video & webinar

Dr. Eletherios Diamandis and Dr. Andrei Drabovich, both of Mount Sinai Hospital and the University of Toronto, Canada, discuss translational proteomics and the difficult of translating biomarker discovery work into diagnostic tests for cancer and other conditions.



The discovery stage of translational proteomics involves the identification and characterization of differentially abundant proteins that are of scientific interest as potential biomarkers. High-resolution accurate-mass (HRAM) mass spectrometry is used to generate the lists of putative biomarkers that can then be verified and validated. Thermo Scientific™ Orbitrap Fusion™ and Q Exactive™ mass spectrometers generate the high-quality, information-rich HRAM data needed for biomarker discovery.Thermo Scientific™ Proteome Discoverer™ software, and Pinpoint™ software are all compatible with HRAM data and can contribute greatly to successful discovery experiments.

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Targeted method development


Verification and validation of putative protein biomarkers involves analyzing fewer, targeted analytes, but analyzing larger numbers of samples. Traditionally the domain of triple quadrupole mass spectrometers, these targeted high-throughput analyses can be performed on a Thermo Scientific™ TSQ-series triple quadrupole mass spectrometer but can also be performed on a high-resolution accurate-mass Q Exactive hybrid quadrupole-Orbitrap instrument. Thermo Scientific™ Pinpoint™ software is designed specifically to facilitate the acquisition of quantitative data and method refinement that takes place during this stage of the workflow.