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Proteomics - pg. 2

Problems in Using Proteomics

Although protein biomarkers hold great promise in our fight against cancer, there are significant challenges that must be overcome:

  • Lack of standardization - Today, laboratories across the country collect, store, and study proteins in different ways. This lack of standardization makes it difficult to accurately compare results from one laboratory to another and limits the number of cancer protein or biomarker tests that are available to the public.
  • The huge number of proteins that exist in the body make it difficult to identify and characterize.
  • Proteins are continually moving and undergoing changes. All of these actions and/or interactions need to be better understood.
  • Proteins exist in a wide range of concentrations in the body. Scientists believe that the most important proteins for understanding and/or detecting cancer may be those found in the smallest concentrations which means being able to detect them is a major problem.
  • As stated earlier most tests today have problems with false positives and false negatives.

Possible Solutions to Problems in Proteomics

  • Scientists have proposed that in order to develop more sensitive and specific cancer diagnostic tests, many biomarkers should be measured simultaneously.

It is thought that patterns revealed in a panel of biomarker proteins associated with a form of cancer - known as a "protein signature" - might have better diagnostic and predictive capabilities than the current singlemarker approach.

Image courtesy of Purdue University, Dr. W. Andy Tao    

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  • To ensure quality laboratory testing, standard collection and testing of samples should be adapted. - Clinical Laboratory Improvement Amandment, (CLIA) labs require this but most research labs do not practice CLIA regulations or hire CLIA licensed employees. Cost is the primary concern. This was never a problem in basic research labs but as research findings have more relevance to patients (biomarkers) this becomes a prime issue.

    All clinical laboratory tests (hemoglobin, cholesterol, white or red blood cell count and 100's of others) that can be used to determine patient status and treatment, by law must be tested following CLIA regulations - biomarkers are not yet required by law to follow CLIA regulations for testing but are moving in that direction.

  • Validate all kits and tests

The Future of Proteomic-Based Research

The accessibility of cancer-related proteins in bodily fluids and tissues has triggered extensive protein-focused research. But a lack of reliable methods for protein identification and measurement has led to pervasive problems with reproducibility and comparability of research results.


The TECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic pattern analysis.

The hope is that cancer prognosis can be accomplished by identifying protein patterns of specific cancers using this device or ones like it.

Image provided by CISN archives. All rights reserved.    

Proteomic Technologies: more about these in the 'How Cancer Is Studied' section

  • Mass Spectrometry: Detects and identifies ever-smaller amounts of proteins.
  • Protein Microarrays: Powerful tools for capturing and measuring proteins from blood and other body fluids and tissues.
  • Nanotechnologies: Greatly expands the capabilities of proteomics, addressing current limitations in selectively reaching a target protein in vivo.
  • Bioinformatics: Enables collection, analysis and sharing of huge amounts of data for inter-institutional studies.
  • Biospecimens: The critical need for research access to large numbers of highquality biospecimens annotated with clinical data.
  • Reagents: A growing need for high-quality, standardized reagents (substances used in experiments) that can improve proteomic technologies' specificity and reproducibility.

Proteomics Research Projects or Efforts:

These projects are included as examples of where the science is leading us.

1. Clinical Proteomic Technologies for Cancer (CPTC): Recognizing the promise of clinical proteomics for personalized cancer care, the National Cancer Institute (NCI) has taken a lead role in elevating the field by launching the Clinical Proteomic Technologies for Cancer (CPTC) initiative in 2006.

The goal of the (CPTC) initiative is to foster the building of an integrated foundation of proteomic technologies, data, reagents and reference materials, and analysis systems to accelerate discovery and clinical research in cancer. To learn more about this organization, go to:

2. Proteome Sciences: This is a for-profit company that offers high output proteomics for diagnostic, prognostic & therapeutic applications.

3. Agilent Technologies: Agilent Life Sciences and Chemical Analysis is a for-profit company. It is a leading global provider of instrumentation, supplies, software and services to the life science and chemical analysis markets. They have a large proteomics division.

4. Dualsystems Biotech: This is a for-profit company that is a leading provider of custom services and products in the field of proteomics.


CISN Summary

  • Proteomics is the study of the proteins in a cell, tissue or organism.
  • Scientists are in the early stages of this work so only a small percentage of the thousands of proteins in human cells have been sequenced or identified.
  • Proteomics technology is being explored for potential use in cancer diagnosis and treatment. This research involves searching for proteins that may serve as biomarkers of early disease, responsiveness to therapy, or indicate the likelihood of relapse after treatment.
  • A high priority of current research efforts is the application of proteomics technology to improving cancer diagnosis and monitoring of patients, in addition to their care.
  • Proteomics can help to find and measure which circulating proteins provide evidence that a drug is or is not working.




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