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
------  	---------
39813		Phosphorylation
9148		Acetylation
5972		N-linked glycosylation
3183		Amidation
1761		Methylation
1695		Hydroxylation
1338		O-linked glycosylation
1135		Ubiquitylation
921		Pyrrolidone Carboxylic Acid
561		Sulfation
503		Sumoylation
452		Gamma-Carboxyglutamic Acid
346		Palmitoylation
192		Myristoylation
156		C-linked glycosylation
156		ADP-ribosylation
140		Citrullination
84		Farnesylation
81		S-nitrosylation
64		Geranyl-geranylation
63		Deamidation
57		Formylation
54		Nitration
39		GPI anchoring
33		Bromination
29		S-diacylglycerol cysteine
20		FAD
9557		Others
67996		Total Characterized
77553		Total Processed

Non-Experimental

------          ---------
Frequency       Modification
------          ---------
98592		N-linked glycosylation
68206		Phosphorylation
24045		Acetylation
8459		Methylation
5802		Palmitoylation
4668		Citrullination
3237		Sulfation
2662		O-linked glycosylation
2392		Amidation
2023		S-diacylglycerol cysteine
1795		Ubiquitylation
1766		Hydroxylation
1384		Pyrrolidone Carboxylic Acid
1311		Myristoylation
1036		Geranyl-geranylation
945		GPI anchoring
806		Sumoylation
804		Gamma-Carboxyglutamic Acid
396		S-nitrosylation
376		Deamidation
300		Farnesylation
251		Nitration
169		ADP-ribosylation
164		FAD
125		Formylation
103		C-linked glycosylation
57		Bromination
10411		Others
231874		Total Characterized
242285		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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