PyMassSpec extension for searching mass spectra using NIST's Spectrum Search Engine

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  • License: GNU Lesser General Public License v3 or later (LGPLv3+) (LGPLv3)
  • Author: Dominic Davis-Foster
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PyMassSpec extension for searching mass spectra using NIST’s Spectrum Search Engine

Usage

You will need to supply your own copy of the NIST Mass Spectral library to use this software.

The main class in this library is the Engine class. This class performs the actual searching. Start by initialising the search engine as follows:

search = pyms_nist_search.Engine(
                FULL_PATH_TO_MAIN_LIBRARY,
                pyms_nist_search.NISTMS_MAIN_LIB,
                FULL_PATH_TO_WORK_DIR,
                )

Where FULL_PATH_TO_MAIN_LIBRARY is the path to the location of your mass spectral library, and FULL_PATH_TO_WORK_DIR is the path to the working directory to be used by the search engine.

A MassSpectrum object can then be searched as follows:

search.full_search_with_ref_data(mass_spec)

This will return a list of tuples consisting of SearchResult and ReferenceData objects for the possible identities of the mass spectrum.

A list of just the SearchResult objects can be obtained with this method:

hit_list = search.full_search(mass_spec)

For each of these hits, the reference data can be obtained as follows:

for hit in hit_list:
        ref_data = search.get_reference_data(hit.spec_loc)

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