Clinical Proteomics pp 209-230

Part of the Methods in Molecular Biology™ book series (MIMB, volume 428)

Label-Free LC-MS Method for the Identification of Biomarkers

  • Richard E. Higgs
  • Michael D. Knierman
  • Valentina Gelfanova
  • Jon P. Butler
  • John E. Hale


Pharmaceutical companies and regulatory agencies are pursuing biomarkers as a means to increase the productivity of drug development. Quantifying differential levels of proteins from complex biological samples like plasma or cerebrospinal fluid is one specific approach being used to identify markers of drug action, efficacy, toxicity, etc. Academic investigators are also interested in markers that are diagnostic or prognostic of disease states. We report a comprehensive, fully automated, and label-free approach to relative protein quantification including: sample preparation, proteolytic protein digestion, LC-MS/MS data acquisition, de-noising, mass and charge state estimation, chromatographic alignment, and peptide quantification via integration of extracted ion chromatograms. Additionally, we describe methods for transformation and normalization of the quantitative peptide levels in multiplexed measurements to improve precision for statistical analysis. Lastly, we outline how the described methods can be used to design and power biomarker discovery studies.

Key Words

relative quantification label-free quantification biomarkers proteomics LC-MS/MS 


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Richard E. Higgs
    • 1
  • Michael D. Knierman
    • 2
  • Valentina Gelfanova
    • 3
  • Jon P. Butler
    • 4
  • John E. Hale
    • 5
  1. 1.School of Life SciencesUniversity of Hertfordshire College LaneHatfieldHertsUK
  2. 2.School of Life SciencesUniversity of Hertfordshire College LaneHatfieldHertsUK
  3. 3.School of Life SciencesUniversity of Hertfordshire College LaneHatfieldHertsUK
  4. 4.School of Life SciencesUniversity of Hertfordshire College LaneHatfieldHertsUK
  5. 5.School of Life SciencesUniversity of Hertfordshire College LaneHatfieldHertsUK

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