NIST MS search¶
Description¶
Feature list methods → Annotation → Search spectra → NIST MS Search
or, for an individual row in a feature table
highlight the row, right-click on the selection and choose Search → NIST MS Search from the pop-up menu.
Info
As of mzmine ≥4.10.6, this module no longer drives the interactive NIST MS Search GUI. It now runs NIST's command line program MSPepSearch directly.
This module searches feature spectra against the libraries of a licensed NIST installation, using NIST's command line program MSPepSearch. It supports two kinds of workflows:
- GC-EI: unit mass electron ionization spectra (or pseudo spectra produced by a
Spectral deconvolution module)
searched against the NIST EI libraries (
mainlib,replib). - MS/MS: accurate mass tandem spectra searched against the NIST tandem libraries
(
hr_msms_nist,lr_msms_nist,apci_msms_nist).
Every library of the required content found in the installation is searched, so libraries do not have to be picked by hand.
Warning
Requires a licensed NIST installation of NIST 17 or newer. NIST returns no library spectra or structures to mzmine, so the mirror plot only shows the input (query) spectrum. Contact mzio.io/nist to obtain the latest NIST library.
Requirements¶
This module relies on an installed NIST MS Search / MSPepSearch installation, which is currently only available for Microsoft Windows.
Parameters¶
The setup dialog groups parameters into General (always shown), MS/MS-specific, and GC-EI-MS-specific, since only one of the two tolerance/merging groups applies depending on the selected search type. A Presets button offers the two recommended workflow configurations ("GC-EI (low resolution)" and "MS/MS (high resolution)") as a starting point; applying a preset keeps the installation directory but resets the feature list selection.
Feature lists¶
The feature lists to search.
NIST installation directory¶
The NIST installation directory, for example C:\NIST26. It must contain the MSPepSearch
subdirectory with MSPepSearch64.exe and the library subdirectories, such as mainlib or
hr_msms_nist. Use the search button next to the field to detect an installation automatically
(drive roots and common program folders are scanned).
Search type¶
The NIST search preset to use. It also picks the libraries and decides which of the parameters below apply:
- Automatic (default) — GC-EI identity if the feature list was built by a spectral deconvolution module, MS/MS otherwise.
- GC-EI identity — unit mass EI spectra against the EI libraries, to find the compound itself.
- GC-EI similarity — the same, but also finds related compounds that are not in the library themselves.
- MS/MS — accurate mass spectra against the tandem libraries.
Merge & select fragment scans¶
Controls how fragment spectra are filtered, merged, and selected before searching (see detailed description). Repeated MS/MS spectra may be merged across multiple data files this way instead of using only the most intense one.
Min cosine similarity¶
The minimum similarity score of a reported hit, on mzmine's 0 to 1 scale (this is the NIST match factor divided by 1000). 0.7 and above is usually considered a good match, 0.9 and above an excellent one. Default: 0.7 (GC-EI preset: 0.75).
Precursor m/z tolerance (MS/MS-specific)¶
MS/MS searches only, ignored by the GC-EI searches. How far the precursor m/z of a library entry may differ from the searched spectrum. It only decides which library entries are compared and does not enter the match factor itself. MSPepSearch takes a single value, so this is either an absolute or a relative (ppm) tolerance, never the maximum of both. Default: 20 ppm.
Fragment m/z tolerance (MS/MS-specific)¶
MS/MS searches only. The product ion m/z uncertainty; unlike the precursor tolerance this one decides which signals count as matched and therefore the match factor itself. NIST recommends 20 ppm or less. Single value for the same reason as the precursor tolerance. Default: 20 ppm.
Integer m/z (GC-EI-MS-specific)¶
GC-EI searches only, ignored by the MS/MS search. How signals of the same nominal mass are combined before searching, because the NIST EI libraries are unit mass:
- Sum (default) — adds their intensities, matching how a unit mass library spectrum reports a nominal mass; needed for accurate mass GC data (GC-QTOF, GC-Orbitrap).
- Maximum — keeps only the most intense signal of the nominal mass.
Unit mass quadrupole data has one signal per nominal mass, so both options are equivalent there.