Posted by: tvasailor | May 24, 2012

Overview “Known Unknowns”

New 9-21-20: 
Wiley MS Master Series, Use of Wiley and NIST EI Libraries with NIST Search

Systematic Process for the Identification of “Known Unknowns” in Commercial Products by GC-MS and LC-MS

Note: Details on other subjects are found in “My Topics” tab under sailboat picture above or on the sidebar links to the right..

Introduction:  In the last 34 years, we have developed a systematic process for the identification of “known unknowns” by GC-MS and LC-MS in commercial products.  We define “known unknowns” as non-targeted species which are known in the chemical literature or mass spectrometry reference databases, but unknown to the investigator.  The process is shown in the following simplified flowchart:


This process is described in detail in the February 2013 copy of LCGC, “MS-The Practical Art.”  The article is entitled:  “Identifying “Known Unknowns” in Commercial Products by Mass Spectrometry.”  A copy with associated ads is shown below:

LCGC PDF with Advertisements

The article originated from work presented at Pittcon in 2012.

NIST Search of EI and CID Spectra:  The initial step in our process utilizes computer searches of EI (GC-MS) or CID (LC-MS) spectra against reference databases using the NIST MS search.  The computer EI searches normally work better than CID ones, but the latter are still very useful.  We employ both purchased, in-house, and internet databases:

We use the NIST and Wiley commercial databases, but there are many other specialty databases that others might find useful.

The NIST search interfaces easily with a wide variety of manufacturers’ data processing and structural drawing programs:


“Spectra-Less” Database Searching:  If the NIST search is not successful, then accurate mass data is used to obtain a molecular formula (MF), a monoisotopic mass, or an average molecular weight.  This data is used to search very large databases such as the CAS Registry (>70 million entries) or ChemSpider (>28 million entries) via web interfaces.  We define them as “spectra-less” databases because they contain no computer-searchable mass spectral data.  We had originally used this approach to search the TSCA database or our Eastman Chemical plant material listing.

The candidate structures from the CAS Registry or ChemSpider searches are prioritized by either the number of associated references or key words.  Other ancillary information such as mass spectral fragments in EI or CID spectra; isotopic abundances, UV spectra; types of ion adductsCI data; number of exchangeable protons;  etc. are used to narrow the list to one structure.  This website has many screenshots (SciFinder1, SciFinder2, ChemSpider) that illustrate these approaches with many examples.

Model EI and CID Spectra from NIST Structure Search:  The NIST MS Search program ranks model compounds employing structural searching of both our commercial and in-house databases.  This is particularly valuable for finding model compounds for a proposed structure found in searches of “spectra-less” databases such as the CAS Registry and ChemSpider.

As noted in the table above, there are ~800,000 structures associated with the EI spectra and 100,000 structures with CID mass spectra in our computer-searchable databases.  We use the NIST MS Interpreter  program to automatically correlate fragment ions in the EI and CID spectra with the component’s substructure.

“No Results” from Process:  There will be non-targeted species in the sample which are “unknown unknowns”, those not found in any reference libraries or “spectra-less” databases.  A few thoughts on their identification are discussed in another section.

Future Improvements Needed:  The approach works well for the majority of our samples which are fairly simple and contain components with molecular weights <500 daltons.  On the other hand, improvements are needed for complex samples and components with molecular weights >500 daltons.

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Posted by: tvasailor | September 21, 2020

NIST’s Suggested Settings for AMDIS Filter Settings

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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 tips from NIST:

AMDIS-Developing Libraries
AMDIS-An Introduction to Extracting HIgh-Quality Spectra from Complex GC/MS Data

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Posted by: tvasailor | September 20, 2020

Wiley/NIST Webinar: Example MS Data Files and Spectra

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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

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Posted by: tvasailor | September 19, 2020

Mass Spec Training from David Sparkman

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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

Posted by: tvasailor | September 11, 2020

Wiley/NIST Webinar YouTube Channel

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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
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

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.

YouTube Videos from Others:

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

Original Wiley Videos:

Webinars recorded by Wiley

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Posted by: tvasailor | August 20, 2020

Most Current User Manuals for NIST Search and AMDIS

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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:



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I presented a 5-part Wiley Webinar Series in August-September, 2020.  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:

YouTube Recordings of Parts I-V

Wiley Website and Recorded Videos

Detailed Handouts including tables of content are shown below:

Part I: Spectral Searches with NIST MS Search-9-27-20
Part II: Structure Searches with MS Search and Using MS Interpreter
Part III:  AMDIS (NIST) for Processing EI Mass Spectral Data Files 9-22-20

Part IV: Advanced NIST Hybrid Search of EI and MS/MS Spectra-9-27-20
Part V: Creating and Sharing User EI and MS/MS Libraries

Other Webinar Resources:

DeltaMass Table for Hybrid Search in EI-9-21-20-202 entries
NIST Suggested Settings for AMDIS-9-20-21
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
AMDIS and NIST Search User Manuals-9-7-20
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

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Posted by: tvasailor | June 29, 2020

Holder 20 For Sale

[Sold to Sailor at Concord Yacht Club, 7/1/2020 in Knoxville, TN]

I had planned on using this boat as my main sailboat for racing.  However, I found another Holder 20.  Thus I would like to sell this one for a very good price.  I am not trying to recoup all my expenses.


Nevertheless, the boat is in very good racing shape and would only some part of the deck painted and slightly sanded.

I have included some pictures and bills for some but not all of the work at the following link:

Pictures of Boat and Some Bills
Note:  Used Slideshow mode in Shutterfly for easy viewing


-long cockpit Holder 20 (much better than short cone for racing!)
-new Genesis Sobstad Lightwave main new ($1,293.00)
-new Genesis  Sobstad Lightwave Headsail new ($1,038.00)
-jib by Slo new
-zippered Sobstad bags for sail storage
-spinnaker bag to hang down below to launch spinnaker from cockpit
-three winches on top of cabin, two in cockpit
-cockpit tent
-new halyards and main sheet
-new hardware blocks for traveler
-epoxy racing bottom by Waters $2,555.00-
-hardware exit plates in mast for internal halyards, deck organizer plate and associated blocks on mast step, deck blocks, spinnaker crane, etc. by Todd Weir $1423.00
-deck reinforced by Todd Weir in mass step area
-stern of boat stiffened on the inside by Todd Weir
-spinnaker with quick disconnect for sheets
-tapered spinnaker sheets with quick disconnects
-twing lines with attached snatch blocks
-through deck twing lines exiting to fairleads/cam cleats in cockpit for easy access and no deck clutter
-trailer with spare tire and poles for guiding boat onto trailer
-backstay flicker on top of mast
-ratchet blocks on stern for spinnaker


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I had the opportunity to present at the ASMS Workshop:  “Compound Identification by Mass Spectral Searching, June 3, 2020.  Unfortunately, there were serious problems with my connection and I was unable to present the information.

Here is a link if you are interested.

ASMS Workshop Presentation



Posted by: tvasailor | February 8, 2019

Bridge Game Links

I have had a really good time playing duplicate bridge with many different people in Kingsport, Abingdon, and Johnson City.

The clubs often offer basic “learn to play (free)” courses led by Jan Bruce and Vivian McIntire.  During the recent “Corona Virus” break, the Abingdon Bridge Club has been hosting  “intermediate” bridge lesson series via Zoom that include all the conventions to facilitate an effective 2 over 1 approach to bridge bidding.

see the Abingdon Facebook site

The internet is also a great “bridge teacher.”

I wanted to share some links that I have found very useful for learning to bid and play.

For standard bridge, the following “cheat” sheet summarizes all basic rules:

Basic Bridge Bidding

The New York City Learn Bridge has great more advanced bidding protocols and tactics for playing hands.

I really like YouTube videos!

New York City Learn Bridge

Phillip Holland does great YouTubes demonstrating bidding and playing hands:

Australian Phillip Holland WebSite

Here is an example of one of his YouTube Videos:

Phillip Holland YouTube Example

Posted by: tvasailor | September 15, 2018

Tesla Cars

I had read the biography of Elon Musk, and decided I couldn’t afford a ride on Space-X.   Therefore, the only logical decision was to instead buy a used Tesla.

I bought a 2014 certified preowned Model S85 in July 2018.  Tried to keep price to minimum by not selecting one with a panoramic roof, air-suspension, and dual wheel drive.

Used Tesla Site

The only problem that I have encountered is that I can’t wipe that silly grin off my face everytime I drive it!  The smooth, quick acceleration is addictive.

Added some information about the car in the following PDF that I put together for a local car show at Allandale.

Model S Tesla Information

Nikola Model S

I added a personalized as a result of a gift a colleague gave me when I retired from Eastman.  The following is a snapshot of my Facebook post:



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