Identification - NIST MS Search

Description

This module allows searching spectra against spectral libraries using the NIST MS Search program.

NIST MS Search accepts spectra as input to its searches. The MS level may be specified to limit a search to MS/MS fragment spectra, clustered spectra produced from any Spectral Deconvolution module, or MS1 precursors ions. The spectra will be searched using the default library search parameters in the NIST MS Search program. To adjust these parameters: open the program, adjust the library search parameters, and save the configuration to a *.INI file. Note - Automation must be enabled in the library search options to enable automatic searching. Be sure all appropriate libraries are included before starting a search.

Repeated MS/MS spectra may be merged between multiple data files using the Merge MS/MS (experimental) module. The input Mass list filters the fragment ions by intensity, and repeatable signals are assessed via cosine dot product.

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 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).
MS level
MS spectra level for searching. Use MS level = 1 to search clustered spectra produced from Spectral Deconvolution modules.
Mass list
MS/MS fragment ion mass list. Use this to specify noise level in acquired MS/MS spectra. Mass list is only used during MS/MS merging - use a dummy list for all other searches.
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.
Merge MS/MS (experimental)
Optional parameter. Merge multiple MS/MS spectra into consensus feature using specified parameters.
Integer m/z
Optional parameter. Convert accurate mass m/z measurements to low-resolution integer values.

Requirements

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