Thu, 21 Aug 2008 14:04:17 BST CiteULike: neils's Campbell http://www.citeulike.org/user/neils/author/Campbell CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2891490 <i>J. Proteome Res. (13 June 2008)</i><br /><br />Abstract: Phosphopeptide identification and phosphorylation site localization are crucial aspects of many biological studies. Furthermore, multiple phosphorylations of peptides make site localization even more difficult. We developed a probability-based method to unambiguously determine phosphorylation sites within phosphopeptides using MS2/3 pair information. A comparison test was performed with SEQUEST and MASCOT predictions using a spectral data set from a synthetic doubly phosphorylated peptide, and the results showed that PhosphoScan analysis yielded a 63% phosphopeptide localization improvement compared with SEQUEST and a 57% improvement compared with MASCOT. PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information Yunhu Wan Diane Cripps Stefani Thomas Patricia Campbell Nicholas Ambulos Ting Chen Austin Yang doi:10.1021/pr700773p J. Proteome Res. (13 June 2008) 2008-06-13T13:53:04-00:00 2008 J. Proteome Res. mass-spec phosphorylation prediction probability http://www.citeulike.org/user/neils/article/2053696 <i>Nucleic Acids Res, Vol. 33, No. Database issue. (Jan 2005), pp. D284-D288.</i><br /><br />PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathways), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. The latest version, 5.0, contains 6683 protein families, divided into 31,705 subfamilies, covering approximately 90% of mammalian protein-coding genes. PANTHER 5.0 includes a number of significant improvements over previous versions, most notably (i) representation of pathways (primarily signaling pathways) and association with subfamilies and individual protein sequences; (ii) an improved methodology for defining the PANTHER families and subfamilies, and for building the HMMs; (iii) resources for scoring sequences against PANTHER HMMs both over the web and locally; and (iv) a number of new web resources to facilitate analysis of large gene lists, including data generated from high-throughput expression experiments. Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com. The PANTHER database of protein families, subfamilies, functions and pathways. Huaiyu Mi Betty Ulitsky Rozina Loo Anish Kejariwal Jody Vandergriff Steven Rabkin Nan Guo Anushya Muruganujan Olivier Doremieux Michael Campbell Hiroaki Kitano Paul Thomas Nucleic Acids Res, Vol. 33, No. Database issue. (Jan 2005), pp. D284-D288. 2007-12-04T01:53:36-00:00 2005 Nucleic Acids Res 33 Database issue D284 D288 article-nar article-pka-pkg database interface panther user-computer