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 ------ --------- 49116 Phosphorylation 5756 N-linked glycosylation 5169 Acetylation 3153 Amidation 1683 Hydroxylation 1625 Methylation 1271 O-linked glycosylation 1014 Ubiquitylation 894 Pyrrolidone Carboxylic Acid 532 Sulfation 452 Gamma-Carboxyglutamic Acid 447 Sumoylation 337 Palmitoylation 191 Myristoylation 155 ADP-ribosylation 152 C-linked glycosylation 83 Farnesylation 77 S-nitrosylation 71 Citrullination 61 Nitration 59 Geranyl-geranylation 56 Formylation 55 Deamidation 37 S-diacylglycerol cysteine 34 GPI anchoring 33 Bromination 20 FAD 8003 Others 72533 Total Characterized 80536 Total Processed
------ --------- Frequency Modification ------ --------- 97593 N-linked glycosylation 72053 Phosphorylation 16523 Acetylation 8060 Methylation 5626 Palmitoylation 4479 Citrullination 2890 Sulfation 2475 O-linked glycosylation 2272 Amidation 1990 S-diacylglycerol cysteine 1771 Ubiquitylation 1764 Hydroxylation 1474 Pyrrolidone Carboxylic Acid 1301 Myristoylation 1039 Geranyl-geranylation 861 GPI anchoring 809 Gamma-Carboxyglutamic Acid 775 Sumoylation 288 Farnesylation 189 S-nitrosylation 169 ADP-ribosylation 165 Deamidation 163 FAD 125 Formylation 108 Nitration 103 C-linked glycosylation 56 Bromination 5141 Others 225121 Total Characterized 230262 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.