MADpipe is a software suite for MRM-assay design that includes:
1) PeptideTracker, a knowledge base, containing empirical information on light and heavy labeled peptides in human and mouse
2) PeptidePicker Library, a pre-compiled library of all possible peptide surrogates for all human proteins [PMID: 26232110]
3) PeptidePicker for selecting proteotypic peptides, based on information about the protein and the suitability of its tryptic peptides for MRM from six on-line knowledge bases [PMID: 24769191]
4) Qualis-SIS, for rapid post-analytical calculation and visualization of MRM data [PMID: 25546269].
All tools use simple data formats allowing easy manipulation and use with each other. To start please enter a list of protein UniProtKB accession numbers in the box below and submit it to MADpipe.
The results will appear in the different tabs according to the available information on these proteins. If a peptide is already in the PeptideTracker knowledge base, empirical information, including best transitions, optimization values, LC gradients and retention times and possibly concentration ranges in biological matrices is already available for use in designing a targeted proteomics assay.
Some of this information, e.g. transitions and retention times are platform-specific. In addition the provided concentrations stem from in-house measurements.
Proteins not in PeptideTracker are likely to be found in the pre-compiled PeptidePicker library that includes 160k suitable surrogate peptides covering the human proteome, alternatively, PeptidePicker software can be used to find current information compiled instantaneously from the major community knowledge bases. After the experiment, the peak areas can be exported from vendor-dependent or -independent (e.g. Skyline) software, and the endogenous and labeled peptide responses can be imported into Qualis-SIS for evaluation and calculation of the final concentrations.