PTM Statistics Curator: Automated Curation and Population of PTM Statistics from the Swiss-Prot Knowledgebase
The PTM Statistics Curator is an automated computational method for quantifying the number of each post-translational modification reported experimentally and non-experimentally in the Swiss-Prot Knowledgebase. Non-experimental qualifiers (Potential, Probable, By Similarity) are consistent with those defined in Swiss-Prot. This method will automatically load the new PTM IDs, curate them, and quantify and even categorize by organism this information every month as the Swiss-Prot Knowledgebase is updated. It was created with the intention of being used at-large as a continuously updated resource for use by the academic community.
Instructions to Download and View the Statistics for Each Individual Modification
How to Cite PTMCurator
Please cite the associated publication, which describes the details of our method.
Khoury, G. A., Baliban, R. C. & Floudas, C. A. Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Sci. Rep. 1, 90; DOI:10.1038/srep00090 (2011).
We have populated the UniProt ID numbers associated with each modification. The files byidexperimental.txt and byidnonexperimental.txt contain the UniProt ID numbers sorted by modification type so one can cross-reference to the Swiss-Prot database for further information. These files have been added to the download link above.
We have added the ability to filter the modification statistics by whether it occurred on a prokaryote (proksexp.txt and proksnonexp.txt) or a eukaryote (euksexp.txt and euksnonexp.txt). We further specify the distribution of the modifications occurring on mammalian proteins in the files mammalexp.txt and mammalnonexp.txt. These files have been added to the download link above.
Note: UniProt has changed its non-experimental qualifiers. We are working to understand how this change affects our code. Currently the code cannot distinguish between experimental and non-experimental modifications, so please refer to our publication for the most accurate estimation of the current state of PTMs as the number of sequences deposited into the Swiss-Prot database has not significantly increased since that date.
------ --------- Frequency Modification ------ --------- 108222 Phosphorylation 104966 N-linked glycosylation 33291 Acetylation 10295 Methylation 6069 Palmitoylation 5548 Amidation 4808 Citrullination 4104 O-linked glycosylation 3842 Sulfation 3259 Hydroxylation 2983 Ubiquitylation 2062 S-diacylglycerol cysteine 1616 Pyrrolidone Carboxylic Acid 1508 Myristoylation 1344 Sumoylation 1257 Gamma-Carboxyglutamic Acid 1098 Geranyl-geranylation 1012 GPI anchoring 477 S-nitrosylation 440 Deamidation 384 Farnesylation 325 ADP-ribosylation 305 Nitration 259 C-linked glycosylation 186 FAD 182 Formylation 87 Bromination 20068 Others 299929 Total Characterized 319997 Total Processed
------ --------- Frequency Modification ------ --------- 0 Palmitoylation 0 C-linked glycosylation 0 Hydroxylation 0 Gamma-Carboxyglutamic Acid 0 S-nitrosylation 0 GPI anchoring 0 Amidation 0 O-linked glycosylation 0 Citrullination 0 Nitration 0 N-linked glycosylation 0 ADP-ribosylation 0 Ubiquitylation 0 Farnesylation 0 Pyrrolidone Carboxylic Acid 0 Methylation 0 Acetylation 0 Phosphorylation 0 Sulfation 0 Bromination 0 S-diacylglycerol cysteine 0 Myristoylation 0 Formylation 0 Sumoylation 0 FAD 0 Deamidation 0 Geranyl-geranylation 0 Others 0 Total Characterized 0 Total Processed
Our PTM Curator performs several algorithmic steps monthly in line with updates from the Swiss-Prot Knowledgebase to generate the results. For a more detailed description of the methods, please refer to our publication below.
Although every consideration has been made during the design, generation, and posting of this data, we provide all data 'as-is'. We make no warranties regarding its correctness, and disclaim liability for damages resulting from its use. This website and associated data and services are for research only, not for clinical or commercial use. We provide this information as a non-profit service to the academic community.