- SRM Quantitation and QC (SmartPeak 2)
- Protein-nucleic acid cross-linking (OpenNuXL)
- Efficient Bayesian protein inference (EPIFANY)
- Top-down proteomics (FLASHDeconv)
- Nucleic Acid Search Engine (NASE)
- Protein-Protein Cross-Linking (OpenPepXL)
- RNA-Protein Cross-Linking (RNPxl)
- Stable Isotope Probing (MetaProSIP)
NASE will be part of the next OpenMS release, 2.5. Until then a custom installer is provided.
To install the software, download and run the installer for your operating system. Installation should only take a few minutes:
The installers include all relevant dependencies. The complete source code is also available in the OpenMS GitHub repository.
Note: On some Windows PCs, the installer may report an error about being unable to install a Visual Studio redistributable package. This warning can be ignored.
- HCD 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.
Preprint available on bioRxiv: https://www.biorxiv.org/content/10.1101/501668v1
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.