Computational expertise in the Protein Research Group
Computational analysis is an integral part of modern proteomics. Within the Protein Research Group, we develop and apply computational approaches for quantitative proteomics, statistical analysis, protein networks, post-translational modifications and the interpretation of complex biological datasets.
Our computational activities range from the development of dedicated software and statistical methods to reproducible workflows for processing and interpreting mass spectrometry-based data. The tools and resources below illustrate this expertise and its development across several generations of proteomics research.
Selected computational tools and resources
| Name | Description | Publication |
|---|---|---|
| PolySTest | Robust statistical testing of quantitative proteomics data. | Schwämmle et al., 2020 |
| HUMOS | eLearning web application developed to support teaching of Orbitrap mass spectrometry. | Bubis et al., 2020 |
| ComplexBrowser | R-based software for supervised analysis of changes in protein-complex abundance and subunit co-expression in proteomics datasets. | Michalak et al., 2019 |
| CoExpresso | Tool for investigating co-regulatory behaviour and its significance among protein subunits in known protein complexes. | Chalabi et al., 2019 |
| ProtProtocols and IsoProt | Containerised workflows for proteomics data analysis. | Griss et al., 2019 |
| Citrullia | Software for confident identification of citrullinated peptides. | Larsen et al., 2020 |
| topdownR | Software for systematic investigation of MS/MS fragmentation methods on Orbitrap instruments and analysis of the resulting spectra. | Shliaha et al., 2018 |
| VSClust | Feature-based variance-sensitive clustering of omics data. | Schwämmle et al., 2018 |
| SuperQuant | Quantitative proteomics data-processing approach using complementary fragment ions to identify and quantify multiple co-isolated peptides in tandem mass spectra. | Gorshkov et al., 2015 |
| A2b2-restrictor | Deconvolution of multiple fragmented peptides using the relationship between a2/b2 and yn-2 ions in HCD spectra. | Kryuchkov et al., 2014 |
| CrossTalkDB | Platform for collecting, statistically assessing and analysing multiply modified proteins and estimating post-translational modification crosstalk. | Schwämmle et al., 2014 |
| PhosphoSiteLocalizer | Approach for phosphosite localisation using complementary peptide fragmentation by CID and ETD. | Hansen et al., 2012 |
| MASSAI | Software for analysis of data from chemical cross-linking experiments. | Rasmussen et al., 2011 |
| GPMAW | Software for analysing proteins and peptides. | |
| GitHub projects | Source code and documentation for current and former software developments. | |
| Bitbucket projects | Source code and documentation for current and former software developments. |
Computational approaches in our research
Computational methods are integrated across research and collaborations within the Protein Research Group. Our expertise supports the analysis of complex proteomics and other omics datasets and connects experimental measurements with quantitative analysis and biological interpretation.