Using bioinformatic resources in the proteomic analysis of biological fluids

On‐line databases targeted towards protein contents in biological fluids are scarce. Consequently, the investigation of proteins identified in a biological fluid most importantly depends on crosschecking information gathered from less specific resources. This review summarises the key databases and tools for collecting information on tissue specificity or expression profiles. It also emphasises the high connectivity between databases fruitfully used to corroborate and piece information together. Finally, selected issues related to appropriate bioinformatics tools in the context of clinical applications are succinctly discussed.

[1]  R D Appel,et al.  SWISS‐2DPAGE: A database of two‐dimensional gel electrophoresis images , 1993, Electrophoresis.

[2]  G A Orr,et al.  Two‐dimensional protein electrophoresis and multiple hypothesis testing to detect potential serum protein biomarkers in children with fetal alcohol syndrome , 1995, Electrophoresis.

[3]  J. Celis,et al.  Towards a comprehensive database of proteins from the urine of patients with bladder cancer. , 1996, The Journal of urology.

[4]  Roberto Raggiaschi,et al.  A two‐dimensional protein map of human amniotic fluid at 17 weeks' gestation , 1997, Electrophoresis.

[5]  Ruddy Wattiez,et al.  Human bronchoalveolar lavage fluid: Two‐dimensional gel electrophoresis, amino acid microsequencing and identification of major proteins , 1999, Electrophoresis.

[6]  R D Appel,et al.  Two‐dimensional electrophoresis resources available from ExPASy , 1999, Electrophoresis.

[7]  I. Thalmann,et al.  Proteomics and the Inner Ear , 2002, Disease markers.

[8]  Andreas Bohne,et al.  SWEET-DB: an attempt to create annotated data collections for carbohydrates , 2002, Nucleic Acids Res..

[9]  N. Anderson,et al.  The Human Plasma Proteome , 2002, Molecular & Cellular Proteomics.

[10]  Rolf Apweiler,et al.  The Proteomics Standards Initiative , 2003, Proteomics.

[11]  Aubrey E. Hill,et al.  The UAB Proteomics Database , 2003, Bioinform..

[12]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[13]  Hiren J. Joshi,et al.  GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003, update , 2003, Nucleic Acids Res..

[14]  Enrico Bertino,et al.  Structural proteome of human colostral fat globule membrane proteins , 2003, Proteomics.

[15]  David Botstein,et al.  SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data , 2003, Nucleic Acids Res..

[16]  Pierre-Alain Binz,et al.  The Make 2D‐DB II package: Conversion of federated two‐dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases , 2003, Proteomics.

[17]  Robert S. Ledley,et al.  The Protein Information Resource , 2003, Nucleic Acids Res..

[18]  L. M. Glodé,et al.  A comprehensive characterization of the peptide and protein constituents of human seminal fluid , 2004, The Prostate.

[19]  Carol S. Giometti,et al.  GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes , 2004, Nucleic Acids Res..

[20]  Barbara A. Wetmore,et al.  Toxicoproteomics: proteomics applied to toxicology and pathology. , 2004, Toxicologic pathology.

[21]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  C. Hoogland,et al.  SWISS‐2DPAGE, ten years later , 2004, Proteomics.

[23]  Kelvin H Lee,et al.  Towards two‐dimensional electrophoresis mapping of the cerebrospinal fluid proteome from a single individual , 2004, Electrophoresis.

[24]  David S. Wishart,et al.  GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images , 2004, Bioinform..

[25]  Jean-Charles Sanchez,et al.  Cystatin C as a potential cerebrospinal fluid marker for the diagnosis of Creutzfeldt‐Jakob disease , 2004, Proteomics.

[26]  E. Birney,et al.  Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Research.

[27]  E. Birney,et al.  The International Protein Index: An integrated database for proteomics experiments , 2004, Proteomics.

[28]  Xuefeng He,et al.  A system for integrative and post-planned analysis of 2-DE/MS centered proteomics data , 2005, J. Integr. Bioinform..

[29]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2005, Nucleic Acids Res..

[30]  William R. Hersh,et al.  A survey of current work in biomedical text mining , 2005, Briefings Bioinform..

[31]  Nichole L. King,et al.  Human Plasma PeptideAtlas , 2005, Proteomics.

[32]  Catherine Brooksbank,et al.  The European Bioinformatics Institute's data resources: towards systems biology , 2004, Nucleic Acids Res..

[33]  Jonas S. Almeida,et al.  AGML Central: web based gel proteomic infrastructure , 2005, Bioinform..

[34]  Erik K. Malm,et al.  A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics* , 2005, Molecular & Cellular Proteomics.

[35]  Johann Joets,et al.  PROTICdb: A web‐based application to store, track, query, and compare plant proteome data , 2005, Proteomics.

[36]  Nichole L. King,et al.  The PeptideAtlas Project , 2010, Proteome Bioinformatics.

[37]  P. Bork,et al.  Literature mining for the biologist: from information retrieval to biological discovery , 2006, Nature Reviews Genetics.

[38]  K. Chisholm,et al.  Targeted comparative proteomics by liquid chromatography/matrix-assisted laser desorption/ionization triple-quadrupole mass spectrometry. , 2006, Rapid communications in mass spectrometry : RCM.

[39]  Lennart Martens,et al.  PRIDE: a public repository of protein and peptide identifications for the proteomics community , 2005, Nucleic Acids Res..

[40]  Kiyoko F. Aoki-Kinoshita,et al.  KEGG as a glycome informatics resource. , 2006, Glycobiology.

[41]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[42]  Peer Bork,et al.  SMART 5: domains in the context of genomes and networks , 2005, Nucleic Acids Res..

[43]  P. Righetti,et al.  Searching for markers of Creutzfeldt‐Jakob disease in cerebrospinal fluid by two‐dimensional mapping , 2006, Proteomics.

[44]  Markus Müller,et al.  Automated protein identification by tandem mass spectrometry: issues and strategies. , 2006, Mass spectrometry reviews.

[45]  D. T. Wong,et al.  Human body fluid proteome analysis , 2006, Proteomics.

[46]  Frédérique Lisacek,et al.  Proteome informatics II: Bioinformatics for comparative proteomics , 2006, Proteomics.

[47]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[48]  Gary D. Bader,et al.  Pathguide: a Pathway Resource List , 2005, Nucleic Acids Res..

[49]  Ron D Appel,et al.  Proteome informatics I: Bioinformatics tools for processing experimental data , 2006, Proteomics.

[50]  Ying Zhang,et al.  HMDB: the Human Metabolome Database , 2007, Nucleic Acids Res..

[51]  M. Girolami,et al.  Clinical proteomics: A need to define the field and to begin to set adequate standards , 2007, Proteomics. Clinical applications.

[52]  Naoyuki Taniguchi,et al.  Comparison of the methods for profiling glycoprotein glycans--HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. , 2007, Glycobiology.

[53]  V. Thongboonkerd Proteomics of human body fluids : principles, methods, and applications , 2007 .

[54]  Jun Adachi,et al.  MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes , 2006, Nucleic Acids Res..