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
------  	---------
39817		Phosphorylation
9116		Acetylation
5996		N-linked glycosylation
3156		Amidation
1782		Methylation
1698		Hydroxylation
1343		O-linked glycosylation
1136		Ubiquitylation
914		Pyrrolidone Carboxylic Acid
580		Sulfation
503		Sumoylation
413		Gamma-Carboxyglutamic Acid
351		Palmitoylation
184		Myristoylation
158		ADP-ribosylation
156		C-linked glycosylation
138		Citrullination
82		Farnesylation
81		S-nitrosylation
63		Deamidation
62		Geranyl-geranylation
57		Formylation
52		Nitration
35		GPI anchoring
30		Bromination
29		S-diacylglycerol cysteine
22		FAD
9566		Others
67954		Total Characterized
77520		Total Processed

Non-Experimental

------          ---------
Frequency       Modification
------          ---------
98732		N-linked glycosylation
68394		Phosphorylation
23929		Acetylation
8496		Methylation
5817		Palmitoylation
4670		Citrullination
3253		Sulfation
2684		O-linked glycosylation
2428		Amidation
2029		S-diacylglycerol cysteine
1798		Ubiquitylation
1794		Hydroxylation
1404		Pyrrolidone Carboxylic Acid
1319		Myristoylation
1036		Geranyl-geranylation
952		GPI anchoring
844		Gamma-Carboxyglutamic Acid
810		Sumoylation
396		S-nitrosylation
376		Deamidation
302		Farnesylation
253		Nitration
167		ADP-ribosylation
164		FAD
125		Formylation
103		C-linked glycosylation
57		Bromination
10422		Others
232332		Total Characterized
242754		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.

url click counter