ArticleMolecular & cellular proteomics : MCP2010
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.
Article in Molecular & cellular proteomics : MCP, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed.
- ProteomeScout v4: An open-source, harmonized, ecosystem for post-translational modifications.bioRxiv : the preprint server for biology · 2026Article
- A global map of associations between types of protein posttranslational modifications and human genetic diseases.iScience · 2021Article
- Future of the Genetic Code.Life (Basel, Switzerland) · 2017Review
- Article
- Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.Nature communications · 2015Article
- ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.Nucleic acids research · 2015Article
- Quantitative Profiling of Lysine Acetylation Reveals Dynamic Crosstalk between Receptor Tyrosine Kinases and Lysine Acetylation.PloS one · 2015Article
- PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis.Database : the journal of biological databases and curation · 2015Article
- Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.Nature neuroscience · 2014Review
- Complexity of metastasis-associated SDF-1 ligand signaling in breast cancer stem cells.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- SysPTM 2.0: an updated systematic resource for post-translational modification.Database : the journal of biological databases and curation · 2014Article
- Proteogenomic convergence for understanding cancer pathways and networks.Clinical proteomics · 2014Review
- Vascular endothelial growth factor (VEGF) and platelet (PF-4) factor 4 inputs modulate human microvascular endothelial signaling in a three-dimensional matrix migration context.Molecular & cellular proteomics : MCP · 2013Article
- Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants.The Biochemical journal · 2013Article
- Mechanosensitive microRNAs-role in endothelial responses to shear stress and redox state.Free radical biology & medicine · 2013Review
- Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice.Integrative biology : quantitative biosciences from nano to macro · 2013Article
- Molecular characterization of EGFR and EGFRvIII signaling networks in human glioblastoma tumor xenografts.Molecular & cellular proteomics : MCP · 2012Article
- Toward quantitative phosphotyrosine profiling in vivo.Seminars in cell & developmental biology · 2012Review
- Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions.Molecular bioSystems · 2012Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs in an effort to facilitate biological understanding of protein modifications in signaling networks. PTMScout is constructed around a custom database of PTM experiments and contains information from external protein and post-translational resources, including gene ontology annotations, Pfam domains, and Scansite predictions of kinase and phosphopeptide binding domain interactions. PTMScout functionality comprises data set comparison tools, data set summary views, and tools for protein assignments of peptides identified by mass spectrometry. Analysis tools in PTMScout focus on informed subset selection via common criteria and on automated hypothesis generation through subset labeling derived from identification of statistically significant enrichment of other annotations in the experiment. Subset selection can be applied through the PTMScout flexible query interface available for quantitative data measurements and data annotations as well as an interface for importing data set groupings by external means, such as unsupervised learning. We exemplify the various functions of PTMScout in application to data sets that contain relative quantitative measurements as well as data sets lacking quantitative measurements, producing a set of interesting biological hypotheses. PTMScout is designed to be a widely accessible tool, enabling generation of multiple types of biological hypotheses from high throughput PTM experiments and advancing functional assignment of novel PTM sites. PTMScout is available at http://ptmscout.mit.edu.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.