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

Note: UniProt has changed its non-experimental qualifiers. We are working to understand how this change affects our code. Currently the code cannot distinguish between experimental and non-experimental modifications, so the experimental statistics below represent the sum of the experimental and non-experimental data with no distinction.

Experimental

------  	---------
Frequency	Modification
------  	---------
108222		Phosphorylation
104966		N-linked glycosylation
33291		Acetylation
10295		Methylation
6069		Palmitoylation
5548		Amidation
4808		Citrullination
4104		O-linked glycosylation
3842		Sulfation
3259		Hydroxylation
2983		Ubiquitylation
2062		S-diacylglycerol cysteine
1616		Pyrrolidone Carboxylic Acid
1508		Myristoylation
1344		Sumoylation
1257		Gamma-Carboxyglutamic Acid
1098		Geranyl-geranylation
1012		GPI anchoring
477		S-nitrosylation
440		Deamidation
384		Farnesylation
325		ADP-ribosylation
305		Nitration
259		C-linked glycosylation
186		FAD
182		Formylation
87		Bromination
20068		Others
299929		Total Characterized
319997		Total Processed

Non-Experimental

------          ---------
Frequency       Modification
------          ---------
0		Palmitoylation
0		C-linked glycosylation
0		Hydroxylation
0		Gamma-Carboxyglutamic Acid
0		S-nitrosylation
0		GPI anchoring
0		Amidation
0		O-linked glycosylation
0		Citrullination
0		Nitration
0		N-linked glycosylation
0		ADP-ribosylation
0		Ubiquitylation
0		Farnesylation
0		Pyrrolidone Carboxylic Acid
0		Methylation
0		Acetylation
0		Phosphorylation
0		Sulfation
0		Bromination
0		S-diacylglycerol cysteine
0		Myristoylation
0		Formylation
0		Sumoylation
0		FAD
0		Deamidation
0		Geranyl-geranylation
0		Others
0		Total Characterized
0		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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