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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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
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

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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:

NIST_Manual_2.4_8-2-20

AMDIS_8-20-20

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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

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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.

$2,300.00

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

List:

-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
-trailer
-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

asms_reboot

 

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

massman_facebook

Another person in Canda not able to get his desired tag:

https://www.cbc.ca/news/canada/saskatchewan/dave-assman-sgi-vanity-licence-plate-1.5017377

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