Posted by: tvasailor | December 11, 2020

LCMS Unknown Identification with NIST Search Using MSMS Libraries

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MS/MS (Tandem) spectra can be used to identify unknowns employing library searches. This is accomplished in much the same approach as that employed for EI GC-MS with the NIST search software. The much improved NIST Search Version 2.4 is included with the 2020 library release. I will attempt to introduce the user to the use of the NIST Version 2.4 search software employing NIST, Wiley, “crowd-sourced (MoNA)”, and user libraries for the identification of unknowns.

NIST has an ambitious program to extend their already comprehensive, high-quality MS/MS databases. See the following link:

NIST Pipeline for Extending MS/MS Libraries

This involves a very comprehensive process for selecting pertinent compounds for purchase and subsequent analyses. The problem with variability of the spectra is reduced by analyzing the samples on a variety of instruments at a variety of energy levels (20 steps). In addition, many different precursor ions and fragment ions are characterized (MSn). This has already led to a very large high quality library of accurate mass MS/MS spectra in the 2020 release version (31K compounds/1.3 M spectra) and the effort is ongoing.

YouTube Videos

Part I: Overview (17 min)
Part II: NIST MS/MS Search (18 min)
Part III: Detailed Discussion Hybrid MS/MS Search (18 min)
Part IV: Importing MSMS Spectra (11 min)
Part V: NIST Structure Searches (12 min)
Part VI: MS Interpreter (12 min)
Part VII: Creating-Using MSMS Libraries (12 min)
Part VIII: “Spectraless Libraries” (12 min)

Higher Quality Videos Zipped Pt. I-VIII

Detailed Handouts

Part I: Overview 12/27/20
Part II: NIST MSMS Search 12/27/20
Part III: Detailed Discussion Hybrid MS/MS Search 12/27/20
Part IV: Importing MSMS Spectra 12-27-20
Part V: NIST Structure Searches 12-27-20
Part VI: MS Interpreter 12-27-20
Part VII: Using-Creating MSMS Libraries 12-27-20
Part VIII: “Spectraless” Libraries 12-27-20

Handouts Pt. I-VIII_Zipped-12-27-20


Using with Manufacturers’ Data Processing Software
Buy a copy! Distributors of NIST Libraries Shop Around for Best Price!
NIST Tandem Quick-Start Guide
DeltaMass Table in Nominal Mass
Beyond the Top Hit: Information from Hybrid Similarity Search Hit Lists
MS_Interpreter Correlating Structure to Spectrum
Lib2NIST (not included with NIST tandem library)
Importing Spectra to NIST Search (all internet links)
Components in MoNA Libraries
MoNA MSMS Library in NIST Format
MoNA EI Library in NIST Format
MoNA Download Site in MSP and SDF Formats
Resources for NIST EI Searches
PowerShell Script for Adding Precursor_m/z Field to User Library
Users’ Manual for NIST 2.4
NIST Downloads Libraries-Tools-Software
NIST MS 2020 at ASMS

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  1. […] The computer EI searches normally work better than CID ones, but the latter are still very useful.  We employ both purchased, in-house, and “crowd-sourced” libraries.  The MoNA “crowd-sourced” libraries in NIST format are found at the following link. […]

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