FLASHIda is an intelligent data acquisition method for top-down proteomics, built for Thermo Scientific tribrids. It ensures the real-time selection of high-quality precursors of diverse proteforms, using an instant m/z-intensity to mass-quality spectral transformation coupled with a machine learning-based quality assessment.
FLASHIda runs as a command-line tool. While running it takes the control over the acquistion of mass spectra, i.e. which spectra will be acquired and in which order. The acquisition parameters can be specified using a XML-formatted method file, an example of it is provided along with the tool.
The following optional arguments can be used
Options:
-h, --help Usage information
-v, --version Show version information
-o, --nocc Ignore contact closure. Default: false
-t, --test Run in test mode without connection to the instrument. Default: false
-m, --method=VALUE Location of method file. Default: method.xml in
the program folder
-r, --rawname=VALUE The name or path to raw file, that will be used to
name the log files. If not specified timestamp
will be used
Advanced usage is discussed in here
- Thermo Scientific tribrid instrument, i.e. Orbitrap Fusion, Orbitrap Fusion Lumos, Orbitrap Eclipse, with Tune version 3.4
- Instrument API - https://github.com/thermofisherlsms/iapi - the API and the license should be obtained separately from Thermo
- .NET 4.8+
- OpenMS libraries
Detailed installation and building instructions
Jeong, K., Babović, M., Gorshkov, V. et al. FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts. Nat Commun 13, 4407 (2022). https://doi.org/10.1038/s41467-022-31922-z