- Intelligent data acquisition for top-down proteomics (FLASHIda)
- Feature level label-free quantification algorithm for top-down proteomics (FLASHDeconvQ)
- SRM Quantitation and QC (SmartPeak 2)
- Protein-nucleic acid cross-linking (OpenNuXL)
- Efficient Bayesian protein inference (EPIFANY)
- Ultra-fast MS1/MS2 deconvolution for top-down proteomics: FLASHDeconv 2.0 beta+, finally with a GUI!
- Nucleic Acid Search Engine (NASE)
- Protein-Protein Cross-Linking (OpenPepXL)
- RNA-Protein Cross-Linking (RNPxl)
- Stable Isotope Probing (MetaProSIP)
Prototype of FLASHDeconvQ, a feature level LFQ algorithm for top-down proteomics, is developed based on OpenMS and FLASHDeconv.