Identification - NIST MS Search

Description

This module allows the identification of chromatographic peaks using the NIST MS Search program.

NIST MS Search accepts spectra as input to its searches. Each spectrum is defined by a list of (mass, intensity) pairs. The module forms a query spectrum for each row in the peak list. For each peak-list row P it finds all other peak-list rows whose (average) RTs are within a specified tolerance (see Spectrum RT tolerance) of P's RT. The peaks' (neutral) mass and intensity value pairs are combined to form a search spectrum for P.

The number of peaks used to form a mass spectrum can be limited by setting the Max. peaks per spectrum parameter to a value greater than zero. If this parameter is set to N then the N rows whose RTs are closest to that of the row (and within the specified RT tolerance) are used to form the mass spectrum.

The module can also be run for an individual row of the peak-list table by highlighting the row and then selecting NIST MS Search from the pop-up menu (right mouse-button click). In such cases, the mass spectrum passed to NIST MS Search is formed in the same way as described above.

Method Parameters

NIST MS Search directory
Full path of the directory containing the NIST MS Search executable (nistms$.exe).
Ionization method
Type of ionization that produced the peak subjected to identification. This is used to calculate the neutral mass.
Spectrum RT tolerance
When forming a search spectrum for a given peak-list row, include all other rows whose (average) RT is within the specified tolerance of the given row.
Max. peaks per spectrum
When forming a search spectrum for a given peak-list row, include at most the specified number of peaks (including the current row). If a row has more than this maximum number of peaks, N, whose RTs are within the specified RT tolerance then it is the N rows whose RTs are closest to that of the row that are used to form the mass spectrum. Setting this parameter to 0 will cause it to be ignored, i.e. all peak-list rows within the specified RT tolerance are used to form the mass spectrum.
Must have same identities
Two peaks will only be included in the same spectrum if they have the same identity (for use with CAMERA pseudo-spectra)
Min. match factor
NIST MS Search calculates a match factor (0 .. 999) between the submitted spectrum and each hit. Ignore hits with a match factor below the given threshold.
Min. reverse match factor
NIST MS Search calculates a reverse match factor (0 .. 999) between the submitted spectrum and each hit. Ignore hits with a reverse match factor below the given threshold.

Requirements

This module relies on the NIST MS Search software, which is currently only available for Microsoft Windows, being installed.