Query: post translational  modification database

title: VPTMdb: a viral post translational modification database
abstract: In viruses, post translational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for better understanding the mechanism of viral infections and finding po tential drug targets. However, a database of comprehensive PTM information on viruses is not available. To fill this gap, we developed a viral post translational modification database (VPTMdb) for collecting systematic information of viral PTM data. The VPTMdb contains 912 PTM sites that integrate 414 experimental confirmed PTM sites with 98 proteins in 45 human viruses manually ex tracted from 162 publications and 498 PTMs extracted from UniProtKB/Swiss Prot. Moreover, we created a novel sequence based classifier named VPTMpre to help users predict viral protein phos phorylated sites. Finally, an online web server was implemented for users to download viral PTM data and predict phosphorylated sites of interest. VPTMdb can be accessed at (http:/vptmdb.com:8787/VPTMdb/

title: Functional analysis tools for post translational modification: a post translational modification database for analysis of proteins and metabolic pathways.
abstract: Post translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post Translational Modifications (FAT PTM) database (https:/bioinformatics.cse.unr.edu/fat ptm/ which currently supports eight different types of PTM and over 49 000 PTM sites identified in large scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT PTM database currently supports tools to visualize protein centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein centric metabolic pathways and groups of proteins that are co modified by multiple PTMs. Overall, the FAT PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.

title: RESTful API for iPTMnet: a resource for protein post translational modification network discovery
abstract: Abstract iPTMnet is a bioinformatics resource that integrates protein post translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and browsing rich PTM information but does not support automated iPTMnet data integration with other tools. Hence, we have developed a RESTful API utilizing the latest developments in cloud technologies to facilitate the integration of iPTMnet into existing tools and pipelines. We have packaged iPTMnet API software in Docker containers and published it on DockerHub for easy redistribution. We have also developed Python and R packages that allow users to integrate iPTMnet for scientific discovery, as demonstrated in a use case that connects PTM sites to kinase signaling pathways.

title: Bioinformatics analysis and collection of protein post translational modification sites in human viruses
abstract: In viruses, post translational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for better understanding the mechanism of viral infections and finding potential drug targets. However, few studies have investigated the roles of viral PTMs in virus human interactions using comprehensive viral PTM datasets. To fill this gap, firstly, we developed a viral post translational modification database (VPTMdb) for collecting systematic information of viral PTM data. The VPTMdb contains 912 PTM sites that integrate 414 experimental confirmed PTM sites with 98 proteins in 45 human viruses manually extracted from 162 publications and 498 PTMs extracted from UniProtKB/Swiss Prot. Secondly, we investigated the viral PTM sequence motifs, the function of target human proteins, and characteristics of PTM protein domains. The results showed that (i) viral PTMs have the consensus motifs with human proteins in phosphorylation, SUMOylation and N glycosylation. (ii) The function of human proteins that targeted by viral PTM proteins are related to protein targeting, translation, and localization. (iii) Viral PTMs are more likely to be enriched in protein domains. The findings should make an important contribution to the field of virus human interaction. Moreover, we created a novel sequence based classifier named VPTMpre to help users predict viral protein phosphorylation sites. Finally, an online web server was implemented for users to download viral protein PTM data and predict phosphorylation sites of interest.  Post translational modifications (PTMs) plays an important role in the regulation of viral proteins; However, due to the limitation of data sets, there has been no detailed investigation of viral protein PTMs characteristics. In this manuscript, we collected experimentally verified viral protein post translational modification sites and analysed viral PTMs data from a bioinformatics perspective. Besides, we constructed a novel feature based machine learning model for predicting phosphorylation site. This is the first study to explore the roles of viral protein modification in virus infection using computational methods. The valuable viral protein PTM data resource will provide new insights into virus host interaction.

title: Proteome wide post translational modification statistics: frequency analysis and curation of the swiss prot database
abstract: Post translational modifications (PTMs) broadly contribute to the recent explosion of proteomic data and possess a complexity surpassing that of protein design. PTMs are the chemical modification of a protein after its translation, and have wide effects broadening its range of functionality. Based on previous estimates, it is widely believed that more than half of proteins are glycoproteins. Whereas mutations can only occur once per position, different forms of post translational modifications may occur in tandem. With the number and abundances of modifications constantly being discovered, there is no method to readily assess their relative levels. Here we report the relative abundances of each PTM found experimentally and putatively, from high quality, manually curated, proteome wide data, and show that at best, less than one fifth of proteins are glycosylated. We make available to the academic community a continuously updated resource (http:/selene.princeton.edu/PTMCuration) containing the statistics so scientists can assess "how many" of each PTM exists.

title: Bioinformatics analysis and collection of protein 1 post translational modification sites in human viruses 2 Analysis of viral protein post translational modification sites 3
abstract: 15 In viruses, post translational modifications (PTMs) are essential for their life cycle. Recognizing 16 viral PTMs is very important for better understanding the mechanism of viral infections and finding 17 potential drug targets. However, few studies have investigated the roles of viral PTMs in virus human 18 interactions using comprehensive viral PTM datasets. To fill this gap, firstly, we developed a viral 19 post translational modification database (VPTMdb) for collecting systematic information of viral PTM 20 data. The VPTMdb contains 912 PTM sites that integrate 414 experimental confirmed PTM sites with 21 98 proteins in 45 human viruses manually extracted from 162 publications and 498 PTMs extracted 22 from UniProtKB/Swiss Prot. Secondly, we investigated the viral PTM sequence motifs, the function of 23 target human proteins, and characteristics of PTM protein domains. The results showed that (i) viral 24 PTMs have the consensus motifs with human proteins in phosphorylation, SUMOylation and 25 N glycosylation. (ii) The function of human proteins that targeted by viral PTM proteins are related to 26 protein targeting, translation, and localization. (iii) Viral PTMs are more likely to be enriched in 27 protein domains. The findings should make an important contribution to the field of virus human 28 interaction. Moreover, we created a novel sequence based classifier named VPTMpre to help users 29 predict viral protein phosphorylation sites. Finally, an online web server was implemented for users to 30 download viral protein PTM data and predict phosphorylation sites of interest.

title: Extending Comet for Global Amino Acid Variant and Post Translational Modification Analysis Using the PSI Extended FASTA Format
abstract: Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is the FASTA format. The Human Proteome Organization's Proteomics Standards Initiative has developed an extension to the FASTA format termed the proteomics standards initiative extended FASTA format or PSI extended FASTA format (PEFF) where additional information such as structural annotations are encoded in the protein description lines. Comet has been extended to automatically analyze the post translational modifications and amino acid substitutions encoded in PEFF databases. Comet's PEFF implementation and example analysis results searching a HEK293 dataset against the neXtProt PEFF database are presented.

title: TCellXTalk facilitates the detection of co modified peptides for the study of protein post translational modification cross talk in T cells
abstract: Protein function is regulated by post translational modifications (PTMs) that may act individually or interact with others in a phenomenon termed PTM cross talk. Multiple databases have been dedicated to PTMs, including recent initiatives oriented towards the in silico prediction of PTM interactions. The study of PTM cross talk ultimately requires experimental evidence about whether certain PTMs coexist in a single protein molecule. However, available resources do not assist researchers in the experimental detection of co modified peptides.  Herein, we present TCellXTalk, a comprehensive database of phosphorylation, ubiquitination and acetylation sites in human T cells that supports the experimental detection of co modified peptides using targeted or directed mass spectrometry. We demonstrate the efficacy of TCellXTalk and the strategy presented here in a proof of concept experiment that enabled the identification and quantification of 15 co modified (phosphorylated and ubiquitinated) peptides from CD3 proteins of the T cell receptor complex. To our knowledge, these are the first co modified peptide sequences described in this widely studied cell type. Furthermore, quantitative data showed distinct dynamics for co modified peptides upon T cell activation, demonstrating differential regulation of co occurring PTMs in this biological context. Overall, TCellXTalk facilitates the experimental detection of co modified peptides in human T cells and puts forward a novel and generic strategy for the study of PTM cross talk. Availability and implementation TCellXTalk is available at https:/www.tcellxtalk.org. Source Code is available at https:/bitbucket.org/lp csic uab/tcellxtalk. Supplementary information Supplementary data are available at Bioinformatics online.

title: Online porous graphic carbon chromatography coupled with tandem mass spectrometry for post translational modification analysis.
abstract: Porous graphic carbon chromatography (PGC) has different mechanism in retention of tryptic peptides compared with reversed phase chromatography and in this study it was shown that coupling PGC with tandem mass spectrometry offer advantages for the quantitation of phosphorylation stoichiometry and characterization of site specific glycosylation.  Digests of protein standards (horse myoglobin, bovine fetuin and b casein) were analyzed with a capillary LC MS/MS system by coupling Agilent 1100 HPLC to Synapt G2 Si HDMS (Waters) Peptides were separated using a HyperCarb PGC column (300 mm i.d.x 100 mm) packing with 3 mm particles. MS/MS data were collected in data dependent mode and 3 MS/MS scans were acquired after full MS scan. RAW data were transformed to.mgf by PLGS (Waters) and searched against Swissprot database by Mascot. Chromatogram and MS/MS spectra of identified were extracted with Masslynx (Waters) and imported to Origin for analysis. Glycan composition and peptide sequence was manually annotated.  PGC MS/MS enabled accurate quantitation of the stoichiometry of specific phosphorylation sites from b casein by efficient separation of the phosphopeptide and its non phosphorylated counterpart, which cannot be achieved by reversed phase chromatography. PGC MS/MS also enabled comprehensive characterization of protein sialoglycosylation as isomeric glycopeptides with different combination of a2 3 and a2 6 linked sialic acids can be separated and the ratio of each combination were verified by exoglycosidase digestion.  PGC has demonstrated superior separation of peptides with phosphorylation and glycosylation and can be used as alternative in proteomic characterization of PTMs by polar groups.

title: Enhanced Global Post translational Modification Discovery with MetaMorpheus.
abstract: Correct identification of protein post translational modifications (PTMs) is crucial to understanding many aspects of protein function in biological processes. G PTM D is a recently developed technique for global identification and localization of PTMs. Spectral file calibration prior to applying G PTM D, and algorithmic enhancements in the peptide database search significantly increase the accuracy, speed, and scope of PTM identification. We enhance G PTM D by using multinotch searches and demonstrate its effectiveness in identification of numerous types of PTMs including high mass modifications such as glycosylations. The changes described in this work lead to a 20% increase in the number of identified modifications and an order of magnitude decrease in search time. The complete workflow is implemented in MetaMorpheus, a software tool that integrates the database search procedure, identification of coisolated peptides, spectral calibration, and the enhanced G PTM D workflow. Multinotch searches are also shown to be useful in contexts other than G PTM D by producing superior results when used instead of standard narrow window and open database searches.