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 ------ --------- 40264 Phosphorylation 7813 Acetylation 5861 N-linked glycosylation 3171 Amidation 1693 Methylation 1691 Hydroxylation 1328 O-linked glycosylation 1106 Ubiquitylation 905 Pyrrolidone Carboxylic Acid 555 Sulfation 472 Sumoylation 452 Gamma-Carboxyglutamic Acid 347 Palmitoylation 192 Myristoylation 156 C-linked glycosylation 155 ADP-ribosylation 92 Citrullination 85 Farnesylation 77 S-nitrosylation 65 Geranyl-geranylation 60 Deamidation 57 Nitration 57 Formylation 38 S-diacylglycerol cysteine 34 GPI anchoring 33 Bromination 20 FAD 8169 Others 66779 Total Characterized 74948 Total Processed
------ --------- Frequency Modification ------ --------- 97940 N-linked glycosylation 66650 Phosphorylation 21623 Acetylation 8329 Methylation 5626 Palmitoylation 4498 Citrullination 3174 Sulfation 2604 O-linked glycosylation 2300 Amidation 1964 S-diacylglycerol cysteine 1778 Hydroxylation 1769 Ubiquitylation 1456 Pyrrolidone Carboxylic Acid 1310 Myristoylation 1035 Geranyl-geranylation 875 GPI anchoring 804 Gamma-Carboxyglutamic Acid 800 Sumoylation 375 Deamidation 354 S-nitrosylation 300 Farnesylation 257 Nitration 169 ADP-ribosylation 163 FAD 125 Formylation 103 C-linked glycosylation 57 Bromination 5138 Others 226438 Total Characterized 231576 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.