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.
------ --------- Frequency Modification ------ --------- 39813 Phosphorylation 9148 Acetylation 5972 N-linked glycosylation 3183 Amidation 1761 Methylation 1695 Hydroxylation 1338 O-linked glycosylation 1135 Ubiquitylation 921 Pyrrolidone Carboxylic Acid 561 Sulfation 503 Sumoylation 452 Gamma-Carboxyglutamic Acid 346 Palmitoylation 192 Myristoylation 156 C-linked glycosylation 156 ADP-ribosylation 140 Citrullination 84 Farnesylation 81 S-nitrosylation 64 Geranyl-geranylation 63 Deamidation 57 Formylation 54 Nitration 39 GPI anchoring 33 Bromination 29 S-diacylglycerol cysteine 20 FAD 9557 Others 67996 Total Characterized 77553 Total Processed
------ --------- Frequency Modification ------ --------- 98592 N-linked glycosylation 68206 Phosphorylation 24045 Acetylation 8459 Methylation 5802 Palmitoylation 4668 Citrullination 3237 Sulfation 2662 O-linked glycosylation 2392 Amidation 2023 S-diacylglycerol cysteine 1795 Ubiquitylation 1766 Hydroxylation 1384 Pyrrolidone Carboxylic Acid 1311 Myristoylation 1036 Geranyl-geranylation 945 GPI anchoring 806 Sumoylation 804 Gamma-Carboxyglutamic Acid 396 S-nitrosylation 376 Deamidation 300 Farnesylation 251 Nitration 169 ADP-ribosylation 164 FAD 125 Formylation 103 C-linked glycosylation 57 Bromination 10411 Others 231874 Total Characterized 242285 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.