Welcome to CrosstalkDB!

This database collects and analyzes mass spectrometry data of multiply modified proteins or long peptide sequences.

We recommend ProteoformQuant (soon to be released) for spectra validation, quantification and data upload.
Users are encouraged to upload their data from mass spectrometry experiments containing multiple modified peptides. Registration is only formal and no private data (not even your email) will be required. After uploading your data, you will still be able to correct errors or delete selected entries.
For details of the database and our view on PTM crosstalk, see our two publications. As there are multiple new features, see also below
Schwämmle, V.; Sidoli, S., Ruminowicz C., Wu X., Lee C. F., Helin K.,and Jensen, O. N. Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation. Mol Cell Proteomics, 2016, 15, 2715-2729
Schwämmle, V.; Aspalter, C.-M.; Sidoli, S. and Jensen, O. N. Large-scale analysis of co-existing post-translational modifications on histone tails reveals global fine-structure of crosstalk Mol Cell Proteomics, 2014, 13, 1855-1865
Rebecca Kirsch, Ole N Jensen and Veit Schwämmle, Methods, 2020


Quantification of PTM crosstalk
Statistics and visualization
Data upload from measurements of multiple modified peptides and proteins
Full data download and API
Soon available: Local version to be run on own computer

We are sure that this software is not exempt from bugs. Please send us a message (at the Feedback page) describing your problem(s).
Statistics of current content
News and Changes

Automatic upload and integration with ProteoformQuant

N-terminal PTMs now allowed.
Internal peptides will be considered correctly.

Simple API and additional statistics on numbers

In the search page, one can now also use URL to specify accession numbers, dataset IDs and PTMs.

New layout of statistics/visualization

The java applet and former figures have been replaced by improved javascript versions
including new representations such as word clouds and a plot of general trends within the
investigated PTMs.

isoScale input and normalization

We now additionally allow input from isoScale.
Two more datasets of mouse stems cell lines added.
Normalization of peptide intensities is carried out over the sum of similar peptides (Levenshtein distance greater than 2). Hence we can assess the crosstalk both of individual histone variants as well as on the entire epigenome (e.g. H3 variants in right proportion).

Quantification upgrade

Quantification is now based on relative abundances (with respect to entire epigenome). Multiple identical entries are merged.
Update to primefaces 5.1

Interface update

Update from Primefaces 4.0 to Primefaces 5.0
Data visualization now works in Firefox
Several changes on data table