Biomarker discovery services

Need to better understand or characterize a disease model?

Do you want to follow the treatment of your patients and confirm proper target engagement?

Liquid biopsy samples, such as serum and plasma, contain all of that information. Our solutions deliver in-depth and robust protein biomarker readouts. Using the Proteograph™ Product Suite for automated sample preparation combined with SWATH™/DIA LC-MS/MS, we reproducibly quantify thousands of proteins and build data insights to advance your project. From functional insights to protein variants and a machine learning development model, our team ensures that the data we generate will get you to the next step.  Our approach is species agnostic and unlike epitope-based technologies, it is truly unbiased.

Using nanoparticles to tackle the complexity of serum/plasma proteomics analysis

Detect more than 5000 proteins in plasma by LC-MS in large cohort. Here’s how.

Most modern data acquisition strategies by LC-MS/MS will only identify 500 to 600 proteins in plasma. Simply put, the depth of analysis one can get from a standard workflow is highly dependent on the dynamic range of the protein concentrations in the sample. The Proteograph™ Product Suite uses nanoparticles (NPs see below) that enable the compression of the dynamic range of protein concentrations in a highly reproducible fashion.  This enables more than 18,000 detected features per sample that allow us to reproducibly (below 15% CV) quantify thousands of proteins across samples including protein isoforms, and even genetic variant pQTLs.  For even more flexibility, we offer gradient options that translate into different yields in the total number of quantified peptides vs. throughput.

Fig. 1  ZenoSWATH-DIA library free output Protein Groups vs. NPs

Nanoparticles: the key to unlocking low-level abundance proteins

Nanoparticles are known for their intrinsic ability to bind proteins. Employing Seer’s Proteograph™ Product Suite for plasma proteomics relies on a library of proprietary engineered nanoparticles to enrich low-abundance proteins. The elegance of this technique is based on the highly reproducible, yet non-specific protein-nanoparticle interactions. Unlike aptamer and antibody-based plasma proteomics methods, plasma fractionation with the Proteograph is species agnostic and can be used for biomarker discovery experiments in non-human samples.

How does it work?

Proteins in the plasma sample are attracted to the nanoparticles to form what is called a protein corona. The composition of the protein corona is affected by different parameters, such as the size, shape, porosity, charge, and surface chemistry of the nanoparticles and the proteins themselves. By using a magnetic core and various surface chemistries, the Proteograph assembles and isolates different protein coronas that span the entire range of protein concentration in plasma. These proteins are then digested into peptides and are ready for analysis using LC-MS/MS. To learn more about Seer’s technology platform visit their website.

Protein Corona Illustration

Fig. 2  Illustration of a protein corona

Data analysis and report

Results from our biomarker discovery using label-free quantitative proteomics experiments are delivered to customers in a user-friendly data report or through the Proteograph™ Analysis Suite. We provide basic statistics such as average, standard deviation, as well as %CV and fold change for each protein to allow direct group comparisons. Additional advanced statistics such as PCAs, volcano plots, heatmap clustering, gene ontology, and more, are also available.

Contact us for your needs in biomarker discovery services

My personal experience of collaborating with PhenoSwitch Bioscience was really amazing and great. Ribosomal protein paralogs have very limited number of amino acid differences. If it were not for PhenoSwitch, it would not have been possible to get such a high quality identification and quantification of duplicated ribosomal proteins in yeast. I am highly indebted and thankful for their perseverance, commitment, help and guidance during the tough times of optimization. If you you need to use MS for identification and quantification of your molecules, I strongly recommend you to talk to these guys!
Mustafa Malik Ghulam, Post Doctoral Fellow, RNA Therapeutic Institute, Umass Medical School, Worcester, Massachussetts

"PhenoSwitch Bioscience Inc has provided us with outstanding efficacious service, high quality data and exemplary data analysis over the past three years."

Stephen Naylor, Ph.D., CEO at ReNeuroGen LCC, Milwaukee, USA
"They have provided excellent data in a timely manner on a number of metabolism and protein studies ongoing in my group"
Klaus Klarskov, Ph.D., Professor at Université de Sherbrooke, Canada
Looking for advice?

PhenoSwitch Bioscience will be happy to help

Are you interested in our services? Please fill out this form and our experts will write back to you in less than 24 hours!

Plan a consultation