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 ------ --------- 39817 Phosphorylation 9116 Acetylation 5996 N-linked glycosylation 3156 Amidation 1782 Methylation 1698 Hydroxylation 1343 O-linked glycosylation 1136 Ubiquitylation 914 Pyrrolidone Carboxylic Acid 580 Sulfation 503 Sumoylation 413 Gamma-Carboxyglutamic Acid 351 Palmitoylation 184 Myristoylation 158 ADP-ribosylation 156 C-linked glycosylation 138 Citrullination 82 Farnesylation 81 S-nitrosylation 63 Deamidation 62 Geranyl-geranylation 57 Formylation 52 Nitration 35 GPI anchoring 30 Bromination 29 S-diacylglycerol cysteine 22 FAD 9566 Others 67954 Total Characterized 77520 Total Processed
------ --------- Frequency Modification ------ --------- 98732 N-linked glycosylation 68394 Phosphorylation 23929 Acetylation 8496 Methylation 5817 Palmitoylation 4670 Citrullination 3253 Sulfation 2684 O-linked glycosylation 2428 Amidation 2029 S-diacylglycerol cysteine 1798 Ubiquitylation 1794 Hydroxylation 1404 Pyrrolidone Carboxylic Acid 1319 Myristoylation 1036 Geranyl-geranylation 952 GPI anchoring 844 Gamma-Carboxyglutamic Acid 810 Sumoylation 396 S-nitrosylation 376 Deamidation 302 Farnesylation 253 Nitration 167 ADP-ribosylation 164 FAD 125 Formylation 103 C-linked glycosylation 57 Bromination 10422 Others 232332 Total Characterized 242754 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.