Return to Home Page

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.

Return to Home Page

Posted by: tvasailor | October 11, 2020

Excel DeltaMass Table for Hybrid Searches

Return to Home Page

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

Return to Home Page

Posted by: tvasailor | October 6, 2020

Agilent Deconvolution Reporting Software (DRS)

Return to Home Page

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

Return to Home Page

Posted by: tvasailor | September 30, 2020

Downloads of NIST Software/Libraries/Tools

Return to Home Page

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:
Downloads

Return to Home Page

Posted by: tvasailor | September 21, 2020

NIST’s Tutorials and Suggested Settings for AMDIS Filters

Return to Home Page

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

Return to Home Page

Posted by: tvasailor | September 20, 2020

Wiley/NIST Webinar: Example MS Data Files and Spectra

Return to Home Page

I used several test files and spectra in the Wiley Webinars to demonstrate the software. I have placed them here if you would like to reproduce my work.

The spectra are stored in a NIST library format. So you must download them and then transfer them to SpecList for searching using the following instructions:

Downloading/Using Example Spectra

Files and Spectra in Zip Files:

Example MS Data Files for Part III AMDIS Webinar
Example Spectra/Structures in Library Format Parts I-V

Return to Home Page

Posted by: tvasailor | September 19, 2020

Mass Spec Training from David Sparkman

Return to Home Page

David Sparkman has trained many in the “art” of mass spectrometry. He is an Adjunct Professor at the University of the Pacific in Stockton, California, and an independent contractor for NIST and Wiley.

Courses and Books

Mass Spec Training Courses

Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation

Gas Chromatography and Mass Spectrometry: A Practical Guide

Mass Spectrometry Desk Reference

Articles and Letters to Editor

Importance of Citing Full Details of Spectral LIbrary and Search Program

Growth of Mass Spec From 1960s to Present: Interview With Professor O. David Sparkman

Posted by: tvasailor | September 11, 2020

Wiley/NIST Webinar YouTube Channel

Return to Home Page

My YouTubes:

I have recorded my own personal versions of the 5-part Wiley webinar series for using NIST software with Wiley and NIST libraries.

Part I: Spectral Searches with NIST MS Search
Part II: Structure Searches with MS Search and Using MS Interpre
ter
Part III: AMDIS (NIST) for Processing EI Mass Spectral Data Files

Part IV: Advanced NIST Hybrid Search of EI and MS/MS Spectra
Part V: Creating and Sharing User EI and MS/MS Libraries

Higher Quality Videos Pt. I-V Zipped

This allowed me to more easily change between different applications while demonstrating the software. In addition, the NIST windows are of higher quality created with my Zoom application versus Wiley’s WorkCast approach.

Original Wiley Videos:

Webinars recorded by Wiley

YouTube Videos from Others:

NIST Basic AMDIS
Agilent DRS -AMDIS/NIST Search/Customer Reports
Importing Shimadzu GC/MS Data into AMDIS and NIST
Accessing NIST Library Search in Agilent GC-MSD

Return to Home Page

Posted by: tvasailor | August 20, 2020

Most Current User Manuals for NIST Search and AMDIS

Return to home page

nist-amdis picI try to keep the most current manuals for AMDIS and NIST MS Search as they are updated.  Sometimes they could appear here before actually updated on NIST site.  Makes it convenient for keeping my links in presentations current.  See the links below:

NIST_Manual_2.4_8-2-20

AMDIS_8-20-20

Return to home page

 

Return to Home Page

GC-MS ID header

I presented a 5-part Wiley Webinar Series in August-September, 2020 on EI library searches.  The series demonstrates the effective use of NIST software such as MS Search, MS Interpreter, and AMDIS with the Wiley, NIST, and user-created libraries.  The following links are for either my personal YouTube or Wiley recordings:

My Personal YouTube Recordings of Parts I-V

Detailed Handouts including tables of content are shown below:

Part I: Spectral Searches with NIST MS Search-12-27-20
Part II: Structure Searches with NIST Search and MS Interpreter-12-27-20
Part III:  AMDIS (NIST) for Processing EI Mass Spectral Data Files 12-27-20

Part IV: Advanced NIST Hybrid Search of EI Spectra-12-27-20
Part V: Creating and Sharing User EI and MS/MS Libraries-12-27-20

Handouts_Pt. 1-Pt. V-zipped_12-27-20

Other Webinar Resources:

Hybrid Search EI example
Using with Manufacturers Data Processing Software
Buy a copy! Distributors of NIST Libraries

DeltaMass Table for Hybrid Search
Importing Mass Spectra to NIST Search Program
NIST Pipeline Program for Adding New Spectra
MS_Interpreter Correlating Structure to Spectrum
NIST Tutorials and Settings for AMDIS-10-15-20
LC-MS/MS Identification of Unknowns with NIST Search

Importance of Library Searches in the Chemical Industry
Example Files for Part III AMDIS Webinar
Example Spectra/Structures in Library Format Parts I-V
Wiley Library User Manual with Spectral Source Codes
NIST Free Downloads of Software/Libraries/Tools-9-29-20
AMDIS and NIST Search User Manuals-9-7-20
NIST MS at ASMS 2020
Description of NIST2020 Software and Library Release by David Sparkman
MS Interpretation Training by David Sparkman

Wiley, NIST, and user-created mass spectral libraries are very powerful tools for the identification of organic compounds in complex mixtures by gas chromatography-mass spectrometry (GC-MS).  This series of seminars will demonstrate the use of the NIST (National Institute of Standards and Technology) software suite for searching these EI libraries.  The software includes MS Search, MS Interpreter, and AMDIS plus ChemSketch for structural drawing. The series should be useful to a wide variety of research and developmental scientists involved in medical, environmental, industrial, forensic, and biological disciplines.

Hybrid Search Resources from Others:

Gary Mallard from NIST a “real-world” example of a fentanyl-related compound from his work.

Hybrid EI Fentanyl Example

Arun Moorthy and Gary Mallard also presented an excellent workshop showing applications of the hybrid search in forensic applications.  The PDF file used in the seminar are shown below.  One will have to register on the website to see the video.

Hybrid vs. Similar Search Slides in PDF:  Identifying Seized Drugs Using Mass Spectral Library Searching
Hybrid vs. Similar Search Webinar:  Identifying Seized Drugs Using Mass Spectral Library Searching

Return to Home Page

« Newer Posts - Older Posts »

Categories