This chapter contains sections titled:

• Introduction

• PPP reference specimens

• Bioinformatics and technology platforms

  • Constructing a PPP database for human plasma and serum proteins

  • Analysis of confidence of protein identifications

  • Quantitation of protein concentrations

• Comparing the specimens

  • Choice of specimen and collection and handling variables

  • Depletion of abundant proteins followed by fractionation of intact proteins

  • Comparing technology platforms

  • Alternative search algorithms for peptide and protein identification

  • Independent analyses of raw spectra or peaklists

  • Comparisons with published reports

  • Direct MS (SELDI) analyses

  • Annotation of the HUPO PPP core dataset(s)

  • Identification of novel peptides using whole genome ORF search

  • Identification of microbial proteins in the circulation

• Discussion

• References