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 ------ --------- 58383 Phosphorylation 6751 Acetylation 5526 N-linked glycosylation 2844 Amidation 1619 Hydroxylation 1523 Methylation 1133 O-linked glycosylation 878 Ubiquitylation 826 Pyrrolidone Carboxylic Acid 504 Sulfation 450 Gamma-Carboxyglutamic Acid 413 Sumoylation 305 Palmitoylation 178 Myristoylation 152 ADP-ribosylation 147 C-linked glycosylation 81 Farnesylation 65 Nitration 62 S-nitrosylation 56 Geranyl-geranylation 55 Citrullination 55 Formylation 53 Deamidation 37 S-diacylglycerol cysteine 34 GPI anchoring 33 Bromination 19 FAD 7208 Others 82182 Total Characterized 89390 Total Processed
------ --------- Frequency Modification ------ --------- 96743 N-linked glycosylation 85499 Phosphorylation 19720 Acetylation 7083 Methylation 5250 Palmitoylation 4448 Citrullination 2691 Sulfation 2335 O-linked glycosylation 2229 Amidation 1923 S-diacylglycerol cysteine 1594 Ubiquitylation 1470 Pyrrolidone Carboxylic Acid 1329 Hydroxylation 1264 Myristoylation 1038 Geranyl-geranylation 845 GPI anchoring 814 Gamma-Carboxyglutamic Acid 696 Sumoylation 280 Farnesylation 165 Deamidation 164 ADP-ribosylation 163 FAD 152 S-nitrosylation 125 Formylation 98 C-linked glycosylation 93 Nitration 56 Bromination 4896 Others 238267 Total Characterized 243163 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.