HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples

Proteomics. 2005 Aug;5(13):3262-77. doi: 10.1002/pmic.200401245.


There is a substantial list of pre-analytical variables that can alter the analysis of blood-derived samples. We have undertaken studies on some of these issues including choice of sample type, stability during storage, use of protease inhibitors, and clinical standardization. As there is a wide range of sample variables and a broad spectrum of analytical techniques in the HUPO PPP effort, it is not possible to define a single list of pre-analytical standards for samples or their processing. We present here a compendium of observations, drawing on actual results and sound clinical theories and practices. Based on our data, we find that (1) platelet-depleted plasma is preferable to serum for certain peptidomic studies; (2) samples should be aliquoted and stored preferably in liquid nitrogen; (3) the addition of protease inhibitors is recommended, but should be incorporated early and used judiciously, as some form non specific protein adducts and others interfere with peptide studies. Further, (4) the diligent tracking of pre-analytical variables and (5) the use of reference materials for quality control and quality assurance, are recommended. These findings help provide guidance on sample handling issues, with the overall suggestion being to be conscious of all possible pre-analytical variables as a prerequisite of any proteomic study.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blood Platelets / chemistry
  • Blood Preservation
  • Blood Proteins / chemistry*
  • Blood Specimen Collection / methods*
  • Computational Biology
  • Electrophoresis, Gel, Two-Dimensional
  • Electrophoresis, Polyacrylamide Gel
  • Female
  • Humans
  • Male
  • Oligonucleotide Array Sequence Analysis
  • Peptides / chemistry
  • Protease Inhibitors / pharmacology
  • Protein Array Analysis
  • Proteomics / methods*
  • Proteomics / standards*
  • Quality Control
  • Reference Standards
  • Reference Values
  • Specimen Handling / methods*
  • Specimen Handling / standards*
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Temperature
  • Time Factors
  • Trypsin / pharmacology


  • Blood Proteins
  • Peptides
  • Protease Inhibitors
  • Trypsin