A functional annotation of subproteomes in human plasma 329

Peipei Ping, Thomas M. Vondriska, Chad J. Creighton, TKB Gandhi, Ziping Yang, Rajasree Menon, Min-Seok Kwon, Sang Yun Cho, Garry Drwal, Markus Kellmann, Suraj Peri, Shubha Suresh, Mads Gronborg, Henrik Molina, Raghothama Chaerkady, B. Rekha, Arun S. Shet, Robert E. Gerszten, Haifeng Wu„ Mark Raftery, Valerie Wasinger, Peter Schulz-Knappe, Samir M. Hanash, Young-ki Paik, William S. Hancock, David J. States, Gilbert S. Omenn and Akhilesh Pandey

16.1 Introduction 330

16.2 Materials and methods 330

16.2.1 Coagulation pathway and protein interaction network analysis 331

16.2.2 Gene ontology annotations 331

16.2.3 Analysis of MS-derived data for identification of proteolytic events and post-translational modifications 331

16.3 Results and discussion 331

16.3.1 Bioinformatic analyses of the functional subproteomes 332

16.3.1.1 An interaction map of human plasma proteins 332

16.3.1.2 Gene Ontology annotation of protein function 334

16.3.2 Proteins involved in the blood coagulation pathway 335

16.3.3 Proteins potentially derived from mononuclear phagocytes 337

16.3.4 Proteins involved in inflammation 338

16.3.5 Analyzing the peptide subproteome of human plasma 339

16.3.6 Liver related plasma proteins 339

16.3.7 Cardiovascular system related plasma proteins 341

16.3.8 Glycoproteins 342

16.3.9 DNA-binding proteins 342

16.3.9.1 Histones 343

16.3.9.2 Helicases 344

16.3.9.3 Zinc finger proteins 345

16.3.10 Annotation through reanalysis of mass spectrometry data 345

16.3.10.1 Cleavage of signal peptides and transmembrane domains 346

16.3.10.2 Identification of PTMs 347

16.4 Concluding remarks 348

16.5 References 349

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