PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

BackgroundIn the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools.DescriptionWe herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified.ConclusionUsing this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.

• Publication year

  2007

• Venue

  BMC Bioinformatics

• Publication date

  2007-12-19

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-8-483PMID 18093328PMCID 2266781
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The unified modeling language reference manual

  2010cited by this paper
• NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

  2006cited by this paper
• Bioinformatic Standards for Proteomics-Oriented Mass Spectrometry

  2006cited by this paper
• A uniform proteomics MS/MS analysis platform utilizing open XML file formats

  2005cited by this paper
• Experimental and bioinformatic approaches for interrogating protein-protein interactions to determine protein function.

  2005cited by this paper
• In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs)

  2005cited by this paper
• Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX

  2005cited by this paper
• NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

  2004influential reference
• Entrez Gene: gene-centered information at NCBI

  2004cited by this paper
• TANDEM: matching proteins with tandem mass spectra.

  2004cited by this paper
• The PARP superfamily

  2004cited by this paper
• Human protein reference database as a discovery resource for proteomics

  2004influential reference
• The Universal Protein Resource (UniProt)

  2004influential reference
• Resolution of Sister Telomere Association Is Required for Progression Through Mitosis

  2004cited by this paper
• Poly(ADP-ribosyl)ated chromatin domains: access granted

  2004cited by this paper
• Common interchange standards for proteomics data: Public availability of tools and schema. Report on the Proteomic Standards Initiative Workshop, 2nd Annual HUPO Congress, Montreal, Canada, 8–11th October 2003

  2004cited by this paper
• The International Protein Index: An integrated database for proteomics experiments

  2004cited by this paper
• MOLECULAR, CELLULAR AND DEVELOPMENTAL BIOLOGY

  2003cited by this paper
• Regulation of chromatin structure and gene activity by poly(ADP-ribose) polymerases.

  2003cited by this paper
• A systematic approach to modeling, capturing, and disseminating proteomics experimental data

  2003cited by this paper
• A statistical model for identifying proteins by tandem mass spectrometry.

  2003cited by this paper
• BIND: the Biomolecular Interaction Network Database

  2003influential reference
• Learning to predict protein-protein interactions from protein sequences

  2003cited by this paper
• Human Proliferating Cell Nuclear Antigen, Poly(ADP-ribose) Polymerase-1, and p21waf1/cip1

  2003cited by this paper
• An integrated proteome database for two‐dimensional electrophoresis data analysis and laboratory information management system

  2002cited by this paper
• DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

  2002cited by this paper
• The challenges ahead.

  2002cited by this paper
• Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

  2002cited by this paper
• Assessment of the reliability of protein-protein interactions and protein function prediction

  2002cited by this paper
• Functional organization of the yeast proteome by systematic analysis of protein complexes

  2002cited by this paper
• Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

  2002cited by this paper
• Personal commentary on proteomics.

  2002cited by this paper
• A comprehensive two-hybrid analysis to explore the yeast protein interactome

  2001cited by this paper
• A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

  2000cited by this paper
• A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae.

  2000cited by this paper
• Systematic and large-scale two-hybrid screens.

  2000cited by this paper
• Identifying the proteome: software tools.

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000influential reference
• Binding of RHOA G17V to p300 enhances its HAT activity: a new mechanism of epigenetic deregulation in TFH lymphoma

  1999influential reference
• Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions.

  1999cited by this paper
• Direct analysis of protein complexes using mass spectrometry

  1999cited by this paper
• Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

  1999cited by this paper
• Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database.

  1995cited by this paper
• Structural and functional analysis of poly(ADP ribose) polymerase: an immunological study.

  1988influential reference

• Metal-organic framework microneedles for precision transdermal drug delivery: design strategy and therapeutic potential.

  2025cites this paper
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  2023cites this paper
• Prediction, Analysis, Visualization, and Storage of Protein–Protein Interactions Using Computational Approaches

  2021cites this paper
• Proteomic Analysis of Merkel Cell Polyomavirus

  2020cites this paper
• Cloud-Based Life Sciences Manufacturing System: Integrated Experiment Management and Data Analysis via Amazon Web Services

  2019cites this paper
• Databases for Protein-Protein Interaction

  2018cites this paper
• Reactive Metabolite Assessment in Drug Discovery and Development in Support of Safe Drug Design

  2018cites this paper
• Parthanatos: Poly ADP Ribose Polymerase (PARP)-Mediated Cell Death

  2018cites this paper
• Nontargeted Identification of Reactive Metabolite Protein Adducts.

  2017cites this paper
• Increasing of Data Security and Workflow Optimization in Information and Management System for Laboratory

  2017cites this paper
• Identification of 4-hydroxynonenal protein targets in rat, mouse and human liver microsomes by two-dimensional liquid chromatography/tandem mass spectrometry.

  2016cites this paper
• Alterations in the proteome of the respiratory tract in response to single and multiple exposures to naphthalene

  2015cites this paper
• Development of Bioinformatics Tools for Biomedical High-Throughput Analyses

  2015cites this paper
• Transcriptional Roles of PARP1 in Cancer

  2014cites this paper
• Utility of the HRN™ (hepatic cytochrome P450 reductase null) mice for investigating mechanisms of liver toxicity of carboxylic-acid-containing drugs

  2014cites this paper
• An Efficient Drug-Target Interaction Mining Algorithm in Heterogeneous Biological Networks

  2014cites this paper
• Efficient Sample Tracking With OpenLabFramework

  2014cites this paper
• Advances in drug-protein adduct analysis Using LC-MS based proteomics

  2013cites this paper
• Protein Adduct Formation by Reactive Electrophiles: Identifying Mechanistic Links with Benzene-Induced Hematotoxicity

  2013cites this paper
• Molecular mechanisms underlying chemical liver injury

  2012cites this paper
• Characterization of Model Peptide Adducts with Reactive Metabolites of Naphthalene by Mass Spectrometry

  2012cites this paper
• Covalent Drug–Protein Adducts: An Exploration of Their Role in Drug‐Induced Liver and General Organ Toxicity

  2012cites this paper
• MolabIS - An integrated information system for storing and managing molecular genetics data

  2011cites this paper
• Sequence tagging reveals unexpected modifications in toxicoproteomics.

  2011cites this paper
• Mass spectrometry-based functional proteomics of poly(ADP-ribose) polymerase-1

  2011cites this paper
• Drug bioactivation and protein adduct formation in the pathogenesis of drug-induced toxicity.

  2011cites this paper
• K-Screen: a free application for high throughput screening data analysis, visualization, and laboratory information management.

  2011cites this paper
• PARP-1 enhances the mismatch-dependence of 5'-directed excision in human mismatch repair in vitro.

  2011influential citation
• Software for supporting large scale data processing for High Throughput Screening

  2011cites this paper
• Protein thiol oxidation in murine airway epithelial cells in response to naphthalene or diethyl maleate.

  2010cites this paper
• Approaches for minimizing metabolic activation of new drug candidates in drug discovery.

  2010cites this paper
• Role of reactive metabolites in drug-induced hepatotoxicity.

  2010cites this paper
• Organization of biomedical data for collaborative scientific research: A research information management system

  2010cites this paper
• PROTEOMER: A workflow‐optimized laboratory information management system for 2‐D electrophoresis‐centered proteomics

  2009cites this paper
• Protein Electrophile-Binding Motifs: Lysine-Rich Proteins Are Preferential Targets of Quinones

  2009cites this paper
• Poly(ADP-ribose) polymerase-1 (PARP-1) longer alleles spanning the promoter region may confer protection to bilateral Meniere's disease

  2009cites this paper
• Metabolites in safety testing (MIST): considerations of mechanisms of toxicity with dose, abundance, and duration of treatment.

  2009cites this paper
• Bioactivation of Drugs by Cytochromes P450 : New Tools and Concepts for the Characterization of Reactive Metabolites of Drugs

  2009cites this paper
• Reactive Metabolite Screening and Covalent-Binding Assays

  2009cites this paper
• Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners

  2009cites this paper
• Liquid chromatography–electrospray tandem mass spectrometry investigations of fragmentation pathways of biliary 4,4′-methylenedianiline conjugates produced in rats

  2008cites this paper
• The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research.

  2008cites this paper
• Protein damage by reactive electrophiles: targets and consequences.

  2008cites this paper
• Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation.

  2008cites this paper
• Protein targets of reactive metabolites of thiobenzamide in rat liver in vivo.

  2008cites this paper
• Role of the peroxynitrite-poly(ADP-ribose) polymerase pathway in human disease.

  2008cites this paper
• Identification and Characterization of Quinone-Thioether Protein Adducts In Vivo

  2008cites this paper