title: PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis.
abstract: Conventional proteomics has discovered a wide gap between protein sequences and biological functions. The third generation of proteomics was provoked to bridge this gap. Targeted and untargeted post-translational modification (PTM) studies are the most important parts of today's proteomics. Considering the expensive and time-consuming nature of experimental methods, computational methods are developed to study, analyze, predict, count and compute the PTM annotations on proteins. The enrichment analysis softwares are among the common computational biology and bioinformatic software packages. The focus of such softwares is to find the probability of occurrence of the desired biological features in any arbitrary list of genes/proteins. We introduce Post-translational modification Enrichment Integration and Matching Analysis (PEIMAN) software to explore more probable and enriched PTMs on proteins. Here, we also represent the statistics of detected PTM terms used in enrichment analysis in PEIMAN software based on the latest released version of UniProtKB/Swiss-Prot. These results, in addition to giving insight to any given list of proteins, could be useful to design targeted PTM studies for identification and characterization of special chemical groups. Database URL: http://bs.ipm.ir/softwares/PEIMAN/
authors.affiliation: Protein Chemistry & Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, 69, Pasteur St., 13164 Tehran, Iran, School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), P. O. Box 193955746, Tehran, Iran and Chronic Kidney Disease Research Center (CKDRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Payman
authors.initials: P
authors.lastname: Nickchi
authors.affiliation: Protein Chemistry & Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, 69, Pasteur St., 13164 Tehran, Iran, School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), P. O. Box 193955746, Tehran, Iran and Chronic Kidney Disease Research Center (CKDRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran Protein Chemistry & Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, 69, Pasteur St., 13164 Tehran, Iran, School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), P. O. Box 193955746, Tehran, Iran and Chronic Kidney Disease Research Center (CKDRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran m_jafari@pasteur.ac.ir mjafari@ipm.ir.
authors.forename: Mohieddin
authors.initials: M
authors.lastname: Jafari
authors.affiliation: Protein Chemistry & Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, 69, Pasteur St., 13164 Tehran, Iran, School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), P. O. Box 193955746, Tehran, Iran and Chronic Kidney Disease Research Center (CKDRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Shiva
authors.initials: S
authors.lastname: Kalantari
mesh_terms: D000818:Animals; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D011499:Protein Processing, Post-Translational; D040901:Proteomics; D012984:Software