Corporate Banner
Satellite Banner
Scientific Community
Become a Member | Sign in
Home>News>This Article

Protein-Measurement Technique’s Could Standardize Quantification of the Human Proteome

Published: Wednesday, December 18, 2013
Last Updated: Wednesday, December 18, 2013
Bookmark and Share
Novel method could alleviate bottleneck in bringing cancer biomarkers to the clinic and increase reproducibility of pre-clinical research.

An international team of scientists led by Fred Hutchinson Cancer Research Center cancer proteomics expert Amanda Paulovich, M.D., has demonstrated the feasibility of large-scale, standardized protein measurements, which are necessary for validation of disease biomarkers and drug targets.

The study, to be published Dec. 8 online in the journal Nature Methods, shows that the scientists’ targeted protein-detection approach has the potential to systematically and reliably measure the entire human repertoire of proteins, known as the proteome.

The technique, developed by Paulovich, a member of Fred Hutch’s Clinical Research Division, and her colleagues, can simultaneously and precisely detect the abundance of hundreds of proteins in many different samples. Researchers from three different groups in Seattle, Boston and South Korea were able to reproduce measurements of 319 proteins from human breast cancer cells, showing that the method can be standardized across laboratory and international boundaries.

“This method has the potential to completely revolutionize how we measure human proteins,” Paulovich said. “Having a global resource for standardized quantification of all human proteins would set new standards that would undoubtedly increase the reproducibility of preclinical research, which would have a dramatic impact on the translation of novel therapeutics and diagnostics.”

Proteins, the molecular workhorses of all biological functions, hold the key to signaling early disease and disease progression. Cancer biomarkers are especially sought after – the protein fingerprints in cells could lead to tests to detect the disease earlier, to identify a person’s specific risk of cancer long before it develops, and to better guide patients’ treatments. But validating newly discovered biomarker candidates has proven impossible without standardized and reproducible methods to measure their levels, Paulovich said.

Each promising biomarker must be further studied in clinical trials, which requires researchers to measure the abundance of each candidate biomarker in hundreds to thousands of patient samples. Because the odds are extraordinarily low that any one candidate will translate to clinical use, large numbers of proteins must be tested to identify a clinically useful biomarker.

“Right now, you can’t make robust measurements of most human proteins,” Paulovich said. “More than 10 years after the human genome has been sequenced and we have the full catalog of molecules as important as proteins, we still can’t study the human proteome with any kind of throughput in a standardized, quantitative manner.”

To address this problem, Paulovich and her colleagues used a sensitive and targeted protein-measurement technology called multiple reaction monitoring mass spectrometry, or MRM-MS. This type of mass spectrometry is not new – it has been used for years in clinical laboratories worldwide to measure drug metabolites and small molecules associated with inborn errors of metabolism. More recently, Paulovich and others have begun using it to measure human proteins.

The researchers’ method enables highly specific, precise, multiplex (meaning the technique measures several different proteins in a single experimental assay) quantification of a minimum of 170 proteins in 20 clinical samples per instrument per day; no other existing technology has this power.

Because the mass spectrometry technique is targeted, meaning the researchers can tune the instruments to look for a specific subset of proteins in cancer cells or other sample types, it can detect the presence of proteins of interest at much lower levels in tiny blood samples or biopsies than a non-targeted tactic.

“The goal is to position this technology to displace some very old technologies that are currently being used,” said Jacob Kennedy, an analytical chemist in Paulovich’s group and lead author of the study.

Currently, researchers usually use either Western blotting, ELISA (enzyme-linked immunosorbent assay), or immunohistochemistry (IHC) techniques to measure levels of proteins in clinical samples. These methods are often not reproducible from laboratory to laboratory, rendering validation of candidate biomarkers for clinical use very difficult, and they cannot be used for large numbers of proteins and samples at once.

Paulovich and her colleagues assayed more than 300 proteins known to be produced by breast cancer cells to validate their technique; their results showed that MRM-MS could recapitulate and extend observations made in previous studies of breast cancer using other technologies.

The study, which included collaborating research groups from the Broad Institute in Cambridge, Mass., and the Seoul National University and Korea Institute of Science and Technology, South Korea, demonstrated MRM-MS’s capacity to measure many proteins at once in a standardized way, laying the foundation for an international, organized effort to quantitate every protein in the human proteome. Their study – the largest to demonstrate the technique’s reproducibility across laboratories and the only international study to do so – has pushed the capacity of the technology the farthest, measuring hundreds of protein pieces where others have measured dozens.

“We really showed what could happen if governments cooperated to build a community resource,” she said. “It’s doable, it’s scalable, and the resource is useful.”

Paulovich’s team hopes the technique catches on in research communities around the world. To facilitate this, her group is spearheading the development of an open-source website to create a centralized resource of highly validated assays for the research community. The portal, funded by the Clinical Proteomics Tumor Analysis Consortium Initiative (CPTAC) of the National Cancer Institute, is set to launch in early 2014.

Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,800+ scientific posters on ePosters
  • More than 4,000+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Scientific News
Developing Drug Resistance may be a Matter of Diversity for Tuberculosis
Researchers have probed the bacteria that causes tuberculosis, Mycobacterium tuberculosis, to learn more about how individual bacterial cells change and adapt while in the human body.
Surprising Trait Found in Anti-HIV Antibodies
Scientists at The Scripps Research Institute (TSRI) have new weapons in the fight against HIV.
Some Gut Microbes May Be Keystones of Health
University of Oregon scientists have found that strength in numbers doesn’t hold true for microbes in the intestines. A minority population of the right type might hold the key to regulating good health.
Essential Component of Antiviral Defense Identified
Infectious disease researchers at the University of Georgia have identified a signaling protein critical for host defense against influenza infection.
Single Vaccine for Chikungunya, Related Viruses May be Possible
What if a single vaccine could protect people from infection by many different viruses? That concept is a step closer to reality.
Is Allergy the Price We Pay for Our Immunity to Parasites?
New findings help demonstrate the evolutionary basis for allergy.
Blocking the Transmission Of Malaria Parasites
Vaccine candidate administered for the first time in humans in a phase I clinical trial led by Oxford University’s Jenner Institute, with partners Imaxio and GSK.
Mucus – the First Line of Defence
Researchers reveal the important role of mucus in building a good defence against invaders.
Antibody Targets Key Cancer Marker
University of Wisconsin-Madison researchers have created a molecular structure that attaches to a molecule on highly aggressive brain cancer and causes tumors to light up in a scanning machine.
Gene-Edited Immune Cells Treat ‘Incurable’ Leukaemia
A new treatment that uses ‘molecular scissors’ to edit genes and create designer immune cells programmed to hunt out and kill drug resistant leukaemia has been used at Great Ormond Street Hospital (GOSH).

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos