title: Enabling proteomics discovery through visual analysis. The peptide permutation and protein prediction tool.
abstract: Proteins play a key role in cellular processes, making proteomics central to understanding systems biology. MS techniques provide a means to observe entire proteomes at a global level. Yet, high-throughput MS proteomics techniques generate data faster than it can currently be analyzed. The success of proteomics depends on high-throughput experimental techniques coupled with sophisticated visual analysis and data-mining methods. Visual analysis has been applied successfully in a number of fields plagued with huge, complex data sets and will likely be an important tool in proteomics discovery. PQuad, a novel visualization of MS proteomics data, provides powerful analysis capabilities that support a number of proteomic data applications. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different protein identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA 99352, USA. susan.havre@pnl.gov
authors.forename: Susan L
authors.initials: SL
authors.lastname: Havre
authors.forename: Mudita
authors.initials: M
authors.lastname: Singhal
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Payne
authors.forename: Mary S Weir
authors.initials: MS
authors.lastname: Lipton
authors.forename: Bobbie-Jo M
authors.initials: BJ
authors.lastname: Webb-Robertson
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D020869:Gene Expression Profiling / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000032:analysis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D049490:Systems Biology / Q000379:methods; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D011506:Proteins