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Mapping the human plasma proteome by SCX-LC-IMS-MS

  • Xiaoyun Liu
  • Stephen J. Valentine
  • Manolo D. Plasencia
  • Sarah Trimpin
  • Stephen Naylor
  • David E. ClemmerEmail author
Focus: From Mobilities To Proteomes

Abstract

The advent of on-line multidimensional liquid chromatography-mass spectrometry has significantly impacted proteomic analyses of complex biological fluids such as plasma. However, there is general agreement that additional advances to enhance the peak capacity of such platforms are required to enhance the accuracy and coverage of proteome maps of such fluids. Here, we describe the combination of strong-cation-exchange and reversed-phase liquid chromatographies with ion mobility and mass spectrometry as a means of characterizing the complex mixture of proteins associated with the human plasma proteome. The increase in separation capacity associated with inclusion of the ion mobility separation leads to generation of one of the most extensive proteome maps to date. The map is generated by analyzing plasma samples of five healthy humans; we report a preliminary identification of 9087 proteins from 37,842 unique peptide assignments. An analysis of expected false-positive rates leads to a high-confidence identification of 2928 proteins. The results are catalogued in a fashion that includes positions and intensities of assigned features observed in the datasets as well as pertinent identification information such as protein accession number, mass, and homology score/confidence indicators. Comparisons of the assigned features reported here with other datasets shows substantial agreement with respect to the first several hundred entries; there is far less agreement associated with detection of lower abundance components.

Keywords

Drift Tube Drift Time Peak Capacity Plasma Proteome Human Plasma Proteome 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Supplementary material

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Copyright information

© American Society for Mass Spectrometry 2007

Authors and Affiliations

  • Xiaoyun Liu
    • 1
  • Stephen J. Valentine
    • 2
  • Manolo D. Plasencia
    • 1
  • Sarah Trimpin
    • 1
  • Stephen Naylor
    • 2
  • David E. Clemmer
    • 1
    Email author
  1. 1.Department of ChemistryIndiana UniversityBloomingtonUSA
  2. 2.Predictive Physiology and Medicine Inc.BloomingtonUSA

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