PTMcosmos is a database that stores post-translational modifications (PTMs) and cancer mutations in humans. It keeps track of supporting evidence for PTMs, which include previous publications, experimental validation and manual curations. It also stores Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomics data, which provides multi-omic profiles from DNA sequencing to protein and PTM mass spectrometry data from cancer and their paired normal samples. Combining PTM and mutation information, PTMcosmos enables users to explore the potential disruption of a PTM function by overlapping or nearby mutations in cancer.
We hope PTMcosmos will serve CPTAC and general research community to better understand the role of PTMs in cancer.
A snapshot of all PTM sites and their number of supporting evidence is released roughly every month. Please refer to the Downloads page.
PTMcosmos is supported by CPTAC and TCGA grants and institutional support.
PTMcosmos was built based on the following data sources:
Visit this repository for the details of CPTAC proteome data preprocessing.
No restrictions are imposed on access to, or use of, the data provided by the HUGO Gene Nomenclature Committee at the European Bioinformatics Institute.
The database is released under Creative Commons Attribution (CC BY 4.0) License. Reference: UniProt: the universal protein knowledgebase. The UniProt Consortium. Nucleic Acids Res. 45:D158-D169 (2017) [PubMed] [Europe PMC]
PhosphoSitePlus (PSP) is licensed by Cell Signaling Technology under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0) License. Reference: PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. Nucleic Acids Res. 43:D512-20 (2015) [PubMed] [Europe PMC]
Reference: Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Kyle Ellrott, Matthew H Bailey, Gordon Saksena, et al. Cell Systems 6:271-281.e7 (2018) [PubMed] [Europe PMC]