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Open Access Highly Accessed Research article

Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications

Chi Nam Ignatius Pang12, Elisabeth Gasteiger3 and Marc R Wilkins12*

Author Affiliations

1 School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia

2 Systems Biology Initiative, University of New South Wales, Sydney, NSW, 2052, Australia

3 Swiss Institute of Bioinformatics, Swiss-Prot Group, CMU - 1, rue Michel Servet, CH-1211 Geneva 4, Switzerland

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BMC Genomics 2010, 11:92  doi:10.1186/1471-2164-11-92

Published: 5 February 2010

Additional files

Additional file 1:

Examples of ambiguous and unambiguous peptide matches. This file contains examples of ambiguous and unambiguous peptide matches.

Format: DOC Size: 40KB Download file

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Additional file 2:

List of lysine- and arginine-methylated peptides. This file contains the list of all high confidence arginine- and lysine-methylated peptides, and their corresponding discovery rates.

Format: XLS Size: 66KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

List of lysine and arginine methylation sites. This file contains the list of all high confidence methylated residues and their corresponding discovery rates.

Format: XLS Size: 43KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Additional benchmarking results. Evaluation of the true positive rates of FindMod using different range of mass tolerance from 0.01 to 0.10 Da, and the known non-redundant methylation test set and the artificial methylation test set.

Format: DOC Size: 108KB Download file

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Open Data

Additional file 5:

List of methylated peptides of Tef1p and Rpl23p discovered by FindMod. This file contains the list of methylated peptides of Tef1p and Rpl23p found by FindMod. These peptides may contain E and D residues, as E and D residues were not filtered for the analysis.

Format: DOC Size: 38KB Download file

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Additional file 6:

Supplementary methods. This file describes how the tailor-made error tolerances was calculated, and also provide a list of low-quality post-translational modifications that were excluded from FindMod's analysis.

Format: DOC Size: 38KB Download file

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Additional file 7:

List of methylation at C-terminus of peptides. This file is a list of peptides with methylation at C-terminus of peptides, collected from literature.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data