Posted by: tvasailor | January 31, 2021

NIST MS Interpreter

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NIST MS Interpreter is a utility developed at the NIST Mass Spectrometry Data Center to assist in the evaluation of mass spectra. The Interpreter finds possible structural origins of peaks in a mass spectrum and provides formula and isotopic processing utilities. It operates in conjunction with the MS Search Program. It works in both nominal and accurate mass modes.

Below are some course resources teaching the use of the program:

Video for EI Use
Handout for EI Use
Video for Tandem Use
Handout for Tandem Use

Below are other resources from NIST:

New Developments Poster
New Enhancements Accurate Mass Tandem Spectra
Basic Description of Program

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Posted by: tvasailor | January 11, 2021

Bread Recipes from Betty Ottenfeld

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In the early 80’s, my Wife Sandra took a bread baking course at the Presbyterian Church. Our family was highly appreciative. Sandra scanned the cookbook handout from the course.

Link to Cookbook Handout in PDF

Picture of Betty, a bird-lover, below:

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Posted by: tvasailor | January 1, 2021

Buying NIST “20” EI and Tandem (MSMS) Libraries

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The new libraries for 2020 include the NIST MS Search Software at no additional cost.

There were major increases in the number of compounds and major software enhancements.

Link to 2020 NIST Updates

The NIST 2020 Tandem library is ridiculously inexpensive, very high quality, and contains 1.3 M spectra!

Be sure to shop around. Here is the total list of distributors:

Total List of Distributors

Here are some good websites that I have noted for distributors. Let me know if you have found others.

Diablo Analytical (convenient same-day ftp download)
Adaptas Solutions (formerly SIS)
Cerno Biosciences
GC Image
MS Wil
Stanton Scientific

The EI library package contains Lib2NIST utility, but not the Tandem one.

Link for Lib2NIST Utility

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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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Posted by: tvasailor | December 11, 2020

Identifying Unknowns Using LCMS and GCMS with Library Searching

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This is a free instructional series including YouTubes, detailed handouts, and miscellaneous resources.

EI GC-MS Identifications: The first part is for EI GC-MS identifications and is accessed at the following link:

Link to EI GC-MS ID of Unknowns with NIST Search

LC-MSMS Identifications: The second part is for LC-MS-MS identifications and is accessed at the following link:

Link to LC-MS-MS ID of Unknowns with NIST Search

Using with Manufacturers Data Processing Software:

Link to Instructions

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Thanks to Wikipedia for Graphics in Header

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Above Image from Wikipedia

The Thermo GC Orbitrap is a very powerful tool for the identification of unknowns easily switching from EI to CI modes. However, one must be aware of the differences in the EI spectra obtained with the Orbitrap compared to standard quadrupole and magnetic spectra found in commercial and user libraries.

The following links shed some insight into those differences from a mechanistic point of view.

Study Comparing 480 Spectra by Eastman for EI

Literature Reference for EI

Two Other Literature References

Literature Reference for Tandem

Thermo and Personal User’s Libraries:

Thermo has and on-going effort to create a database of EI GC-Orbitrap spectra. Release Version 1.0 contains 766 spectra. They are spectra of contaminants related to PCB’s, environmental contaminants, and pesticides.

A user should also consider adding spectra to their personal NIST library noting the origin of the spectrum. I believe that in 70-80% of the cases the hit will be lower (700-800 fit). If no other spectrum from a standard quadrupole is present, the user will still find the EI orbitrap spectrum at the top of the list. Smaller MW compounds and TMS derivatives might be more confusing yielding much lower hits.

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Posted by: tvasailor | October 11, 2020

Excel DeltaMass Table for Hybrid Searches

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The Excel spreadsheet of DeltaMass values is very useful for determining the identity of a compound in a NIST hybrid EI or tandem library search. The values listed in the spreadsheet are common ones that I have found in my evaluation of EI library spectra. They are also finding to be useful in accurate mass Tandem (MS/MS) hybrid searches in LC-MS analyses.

An odd DeltaMass value is indication that the number of nitrogens has changed by an odd number. Similar to nitrogen rule for molecular ions and their fragments in EI interpretation. Currently in nominal mass, but would be nice to have in accurate mass in future!

Excel DeltaMass Table (June 2021, 594 entries)

Free Training Videos and Associated Handouts

YouTube Advanced NIST Hybrid Search of EI Spectra
YouTube Advance NIST Hybrid Search for MS/MS (Tandem) Spectra
Handout NIST Hybrid Search of EI Spectra
Handout NIST Hybrid Search of Tandem (MS/MS) Spectra

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Posted by: tvasailor | October 6, 2020

Agilent Deconvolution Reporting Software (DRS)

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Agilent DRS combines Chemstation-like software with AMDIS and NIST search to generate customer reports of target compound analyses.

Link to Software Products

Links to YouTube Videos

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Posted by: tvasailor | September 30, 2020

Downloads of NIST Software/Libraries/Tools

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All these resources can be found at:
NIST Libraries/Tools/Service Web Site

NIST Search Software 2.3 Version (2017) and Demo Library:
Download Installation Program

MS Interpreter Version 3.4:
Download Version 3.4

AMDIS Version 2.73:
Download AMDIS

Free Libraries and Tools:

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Posted by: tvasailor | September 21, 2020

NIST’s Tutorials and Suggested Settings for AMDIS Filters

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Gary Mallard wrote a series of articles including suggested filter settings in AMDIS. In my work, I have found these filter settings to be very useful for limiting the number of peaks deconvoluted.

The links are noted at the bottom of this post for the series of articles. I have captured the suggested filter settings and his comments below which were found in Figure 4 for Part 3 of his series.

AMDIS: Setting Up and Running a Deconvolution and Target Analysis-Part 1
AMDIS: Setting Up and Running a Deconvolution and Target Analysis-Part 2
AMDIS: Setting Up and Running a Deconvolution and Target Analysis-Part 3

Other AMDIS tips from NIST:

Developing Libraries
Extracting HIgh-Quality Spectra from Complex GC/MS Data
Determining Retention Indices Powerpoint
Determining Retention Indices Text Explanation

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