Discovery Based Proteomics


  • Detection and quantification of many thousands of proteins from hundreds of fluid and tissue samples.
  • Human, rodent, monkey, pig and other higher animal species are covered.
  • By using an upfront high abundance protein depletion stage, we can quantify significantly more lower abundant proteins.
  • Sample multiplexing in a single TMT multiplexed based mass spectrometry run significantly increases the sensitivity of low abundance protein detection.
  • Compatibility with a wide variety of sample matrices, including tissue, serum, cell lysates, CSF, exosomes, etc.
  • Ability to enrich for specific protein subsets, such as secreted proteins, phosphopeptides and other post translational modifications and membrane proteins.
  • Includes full computational proteomic analysis and bioinformatics covering extensive data interpretation, pathway analysis and biological relevance.

Available services are as follows.   
Please contact if you are looking for something in addition analysis wise.

Application Service Description
Fluid Biomarker Discovery Super Depletion
TMT based LC-MS2
TMT based LC-MS3
  • Highest level of abundant protein depletion
  • Highest sample multiplexing – TMTpro 18-plex
  • From 10 to 100+ samples
  • Tissue-enhanced low abundance fluid proteomics
  • Most accurate TMT-MS3 based quantification
Disease Profiling and Target Discovery SysQuant
TMT based LC-MS2
TMT based LC-MS3
  • Enriched PTM proteomics
    • phosphorylation
    • acetylation
    • methylation
    • hydroxylation
    • ubiquitylation
    • glycosylation
    • others on request
  • Highest sample multiplexing – TMTpro™ 18-plex
  • Most accurate TMT- MS3based quantification
Target Engagement and Mechanism of Action Analysis SysQuant
TMT based LC-MS2
TMT based LC-MS3
PRM/SRM Targeted Assays
  • Enriched PTM proteomics
  • Highest sample multiplexing – TMTpro- 18-plex
  • Most accurate TMT-MS3 based quantification
Translational Biomarkers Super Depletion
TMT based LC-MS2
TMT based LC-MS3
  • Combined cross-species tissue/fluid TMTcalibrator
  • In silico comparisons between animal and human studies

Protein biomarkers have broad application across healthcare. Early detection and staging of disease is vital for emerging precision medicine strategies and their use in drug development is showing promise in reducing attrition rates and allowing patient stratification in clinical trials of targeted therapies. Investing early in the identification of as many relevant biomarkers as possible enhances the chance for successful clinical trials.

The heart of any proteomic study initially starts with a discovery phase to identify for instance protein biomarkers that change with the onset of disease, disease progression, drug treatment etc.   Once candidate biomarkers are identified usually you would enter a validation phase with a larger cohort of samples to ensure the validity of the biomarkers in the class comparisons under investigation. Once a fit for purpose set is validated, we can move out of the discovery phase and design a suitable Targeted SRM or PRM assay that aims to be both faster and offer a more cost effective per sample price. With SRM these assays can also be offered under GCLP certification required for later phases in clinical trials.

Proteome Sciences offers unbiased proteomic discovery in combination with both TMT®11-plex and TMTpro 18-plex reagents.  This combined with our expertise in sample preparation, mass spectrometry, bioinformatics, biostatistics and biological interpretation enables discovery of upwards of 10,000 proteins in your samples (dependant on the sample type and sample prep methods used).  These proteins can be of course both known and novel, biologically and clinically relevant proteins.   In many situations both proteins and the PTM’s will be detected.  We aim to sequence and report all quantified proteins, and search on request for applicable PTM classes.


Proteome Sciences unbiased TMT based services aide both the identification and validation of protein biomarkers in the following areas

  • Identification of underlying biology and mechanism of action
  • Disease diagnosis and monitoring of disease progression
  • Patient stratification
  • Monitoring of drug efficacy
  • Development of surrogate endpoints

Sample types

  • Primary tissues
  • Cell culture
  • Cell lysates
  • Fluids to include serum, plasma, CSF, urine and others.  Please enquire
  • Exosomes

Typical Metrics (cell culture / tissues)

  • Over 8,500 quantified proteins
  • If applicable, 15 to 20,000 quantified phosphopeptides
  • 1,000,000 quantitative measurements

Discovery work is performed under ISO 2001-2015

For FAQ’s on Unbiased Protein Biomarker Discovery based Proteomics please follow this link.

Measuring Proteins for Better Medicines