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

Download and unzip the most recent statistics. The statistics can be opened with WordPad, Excel, or TextPad.

DOWNLOAD THE FULL RAW AND SUMMARIZED STATISTICS HERE.

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).

NEW FEATURE

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.

NEW FEATURE

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.

Summarized Statistics

Experimental

------  	---------
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

Non-Experimental

------          ---------
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

Curation Methods

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.

Disclaimer

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.

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