NASE is now included in OpenMS release, 2.5.
Requirements:
- 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.
Publication:
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
Example data:
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.
Example workflow:
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.