- 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)
NASE is now included in OpenMS release, 2.5.
- HCD (or ETD) data of RNA oligonucleotides acquired on a high-resolution mass spectrometer
- Fragment spectra (MS/MS) need to be centroided (either on acquisition, conversion, or in a workflow using the TOPP tool PeakPickerHiRes)
- Developed and tested on Linux (Ubuntu 18.04 and 18.10) systems with data from orbitrap instruments
- Operating system: OpenMS installers have been tested on Ubuntu Linux 18.04, Windows 7/8/10, and macOS 10.12-10.14. If you experience any troubles don’t hesitate to contact the OpenMS team on Gitter chat or open an issue in the OpenMS GitHub repository.
Wein, S., Andrews, B., Sachsenberg, T. et al. A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nat Commun 11, 926 (2020). https://doi.org/10.1038/s41467-020-14665-7
Mass spectrometry data and analysis results from four validation datasets have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifiers PXD012094, PXD016308, PXD016323, and PXD016328.
This workflow can be used to reproduce the results from the PXD016308 dataset. Both input files and expected output files are available in the dataset. Runtime should be less than a minute. Usage instructions for TOPPAS can be found here.