Quandenser (QUANtification by Distillation for ENhanced Signals with Error Regulation) uses a Quantification-first approach for protein quantification in which quantification data is condensed prior to interpretation. We first cluster both MS1 and MS2 information prior to submitting the fragment spectra to the search engine. This allows us to retain all useful information without being limited by the sensitivity of the search engine and reveals analytes of interest that would otherwise be overlooked.
Examples, binaries and installation guides are available on the GitHub page.
Publication: The, M., Käll, L. (2018). “Focus on the spectra that matter by clustering of quantification data in shotgun proteomics.” bioRxiv.