This chapter contains sections titled:

• Introduction

• Materials and methods

  • Coagulation pathway and protein interaction network analysis

  • Gene ontology annotations

  • Analysis of MS-derived data for identification of proteolytic events and post-translational modifications

• Results and discussion

  • Bioinformatic analyses of the functional subproteomes

    • An interaction map of human plasma proteins

    • Gene Ontology annotation of protein function

  • Proteins involved in the blood coagulation pathway

  • Proteins potentially derived from mononuclear phagocytes

  • Proteins involved in inflammation

  • Analyzing the peptide subproteome of human plasma

  • Liver related plasma proteins

  • Cardiovascular system related plasma proteins

  • Glycoproteins

  • DNA-binding proteins

    • Histones

    • Helicases

    • Zinc finger proteins

  • Annotation through reanalysis of mass spectrometry data

    • Cleavage of signal peptides and transmembrane domains

    • Identification of PTMs

• Concluding remarks

• References