Quickstart

Quickstart

See the following information to quickly start searching your proteomics data with ANN-SoLo. This assumes that ANN-SoLo has already been installed.

ANN-SoLo is a spectral library search engine, so you need the following two files:

• A spectral library in the .splib format (for example, generated by SpectraST).
• The spectra to be identified in the .mgf format.

The minimum parameters you need to provide for your search are the following:

• The precursor tolerance mass and mode (either 'Da' or 'ppm'). If only a single precursor mass tolerance is provided a standard search will be performed. The cascade search strategy can be used by giving a second precursor mass tolerance for its second stage as well.
• The fragment mass tolerance (in Dalton).

These minimal parameters can be used to run ANN-SoLo as follows:

ann_solo --precursor_tolerance_mass 20 --precursor_tolerance_mode ppm --precursor_tolerance_mass_open 500 --precursor_tolerance_mode_open Da --fragment_mz_tolerance 0.02 spectral_library.splib spectra.mgf output.mztab

The identifications results will be stored in the mzTab file output.mztab.

See the detailed instructions for more advanced usage and available parameters.