ProteoCombiner: Integrating top-down, bottom-up and middle-down proteomics data

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ProteoCombiner can be freely downloaded and installed with a single click on the Download button.

Publication Details

RAW and result files^* (for top-down and bottom-up proteomics approaches) can be downloaded at PRIDE Repository.
We use a FASTA database for performing bottom-up search on Patternlab for Proteomics and MaxQuant, and an XML database for performing top-down search on ProSight (top-down). Both databases contain the same sequences of E. coli. and can be downloaded here or also at PRIDE Repository.
ProteoCombiner output file (*.pcmb) can be downloaded here.
Example of input files can be downloaded here.

^* Patternlab for Proteomics result file (for bottom-up proteomics results) can be downloaded here.

The source code is available on bitbucket.

⇒ A computer with at least 8 GB RAM and 2 computing cores is recommended.

⇒ Windows 10 (64 bits) or later.

⇒ The .NET framework 4.8, which will be automatically updated by ProteoCombiner if necessary.

⇒ ProteoCombiner v1.0 is compatible with output data files of PatternLab for Proteomics, MaxQuant, Comet, or any other bottom-up search engines that export their results to mzIdentML 1.2 format proposed by HUPO Proteomics Standards Initiative, and ProsightPD, pTop, TopPIC for top-down proteomics approach. In addition, the tool is able to read original Thermo® RAW files.

⇒ ProteoCombiner saves results to its own format (i.e., *.pcmb) and exports to Excel® (*.xlsx) and PDF® format files.