"Little" Mass Spec and Sailing

Access and Origin of Information on Web Page

tvasailor — Sun, 28 Aug 2011 22:07:38 +0000

All the topics are listed as links on the right side of this web page.

The information is a compilation of various topics from posters presented at ASMS and some of our publications over the last 20-30 years. It replaces my discontinued webpage (see info below).

Any questions, contact me at: jameslittleremovethisbeforeemailing@eastman.com

NOTE: modified email above to avoid spam, remove the part “removethisbeforeemailing” from address before sending email!

Hope you enjoy your visit on my webpage!

Using NIST Search Program with Data Processing and Drawing Programs

tvasailor — Sun, 28 Aug 2011 22:04:13 +0000

NIST has greatly facilitated the utilization of the NIST Version 2 library search software package with a wide variety of other data processing and structural drawing packages.

The NIST Version 2.0 installer includes the option to install software to link the GC-MSD data processing software to the NIST V2.0 library search software. I routinely use AMDIS and have tested Wsearch for processing data and transferring spectra to the NIST Ver. 2 search. AMDIS is installed with the NIST search software and Wsearch can be obtained through the link below:

http://www.wsearch.com.au/

I have included some links with instructions to setting up several of these programs below:

Agilent MassHunter:

http://littledomain.com/james/files/agilent_masshunter_nist.pdf

MassLynx:

http://littledomain.com/james/files/masslynx.pdf

Xcalibur:

http://littledomain.com/james/files/xcalibur.pdf

Various Structural Drawing Packages:

http://littledomain.com/james/files/structure_import_export.pdf

Agilent LC-MSD software:

http://littledomain.com/james/files/agilent_lc_msd.pdf

ACD Software:

http://littledomain.com/james/files/acd_fix.pdf

Using New NIST Exact Mass Search to Identify “Known Unknowns”

tvasailor — Sat, 27 Aug 2011 19:43:22 +0000

David Sparkman and Steve Stein showed me some new exact mass search capabilities introduced with the NIST 11 Library at ASMS conference in Denver. They thought that these new capabilities might be useful in the identification of “known unknowns.”

An unknown to an investigator, in many cases, is often known in the chemical literature. We refer to these types of compounds as “known unknowns.” The term originated from a quote by Donald Rumsfeld:

http://en.wikipedia.org/wiki/There_are_known_knowns

I evaluated the software using a group of compounds that I had employed previously to evaluate ChemSpider and CAS. The results were very encouraging. I have attached my initial results and some instructions for searching Warfarin’s exact mass. The approach was very successful for drugs, pesticides, natural products. However, many polymer antioxidants and UV stabilizers were not found. Thus, the choice of which database to search, NIST/ChemSpider/or CAS, will be dependent on the user’s needs.

We heavily use NIST for searching both our EI and MS/MS and searching commercial EI and MS/MS databases. The current version of NIST includes 64,511 MS/MS spectra that can be very useful for identifying “known unknowns.” Furthermore, we routinely run the same sample by LC-MS and GC-MS and utilize EI spectra in addtion to our in-source MS/MS spectra.

David Sparkman mentions these capabilities on page 6 of the following PDF file in a series of articles he has recently published on the internet:

http://www.sepscience.com/emails/MSSol13AP.pdf

Here is a file showing how to use the new NIST exact mass search for identifying a “known unknown” by accurate mass. Of course, one can also search by molecular formula.

http://littledomain.com/james/files/example_web.pdf

Here are the results from my evaluation with 90 compounds:

http://littledomain.com/james/files/nist_evaluation_web.pdf

Links for our two papers describing our work with CAS and ChemSpider are shown below:

http://www.littledomain.com/james/files/known_unknowns_article.pdf

http://littledomain.com/james/chemspider_prepress_ver_6.pdf

Accurate Mass Measurements: Identifying “Known Unknowns” Using ChemSpider

tvasailor — Sun, 22 May 2011 12:47:19 +0000

http://en.wikipedia.org/wiki/There_are_known_knowns

ChemSpider is a very valuable source of known substances. It contains ~25 million compounds which can be searched by a variety of parameters and includes valuable links to other web-based resources. ChemSpider is owned by the Royal Society of Chemistry (RSC) and provided as a free resource to the community.

Modifications in the web-based interface were made to facilitate the entry of monoisotopic molecular weight data and to sort the entries by the number of associated references. The ability to sort by the number of references was demonstrated to be very useful in bringing the most likely candidates to the top of the list. A similar approach was previously demonstrated utilizing the CAS Registry which was searched by either SciFinder or STN Express.

Link to ChemSpider Prepress Journal Article

http://littledomain.com/james/chemspider_prepress_ver_6.pdf

Journal of The American Society for Mass Spectrometry, Volume 23, Number 1, 179-185, DOI: 10.1007/s13361-011-0265-y

Link to ASMS Poster at ASMS Conference 2011, Denver, Colorado:

http://littledomain.com/james/files/asms_poster_single_sheet.pdf

Link to previous work with CAS Registry/SciFinder/STN Express:

http://littlemsandsailing.wordpress.com/2011/05/01/unknown-identification-known-unknowns-with-accurate-mass-mass-spectrometry/

Link to Work with NIST and New Exact Mass Software in Version 11:

http://littlemsandsailing.wordpress.com/2011/08/27/using-new-nist-exact-mass-search-to-identify-known-unknowns/

Unusual Doubly Charged Ion in EI Spectrum of Phosphate

tvasailor — Sun, 01 May 2011 21:51:52 +0000

Normally doubly charged ions are relatively small in electron impact mass spectra. However, we noted one that was almost the base peak in a phosphate!

See the following link for details:

http://www.littledomain.com/james/files/doubly.pdf

Dead-time Correction Limitations on Time-of-flight Mass Spectrometers

tvasailor — Sun, 01 May 2011 17:54:17 +0000

We don’t have extensive information on the long-term precision and accuracy of our TOF instruments. However, we have performed some basic studies to understand the limitations of the LCT and GCT. Our instruments are based on TDC (time-to-digital converters), which affects the accuracy and the precision of the instruments. The TDC approach has two significant limitations:

1) When two or more ions hit the detector in one flight cycle the TDC counts them as one event.

2) When two ions hit the detector within a certain time interval, the TDC does not count the second ion (dead time loss)

The LCT and GCT correct for this problem via software. Our ASMS poster session addresses these limitations and Excel ”program” models the effect.

http://www.littledomain.com/james/files/deadtime_poster.pdf

http://www.littledomain.com/james/files/deadtime_model.xls

Here is a good literature reference that discusses the topic:

Chernuschevich, I. V.; Loboda, A. V.; Thomson, B. A. Special Feature Tutorial: An Introduction to Quadrupole-Time-of-Flight Mass Spectrometry. J. Mass Spectrom. 2001, 36, 849-865.

http://www.spectroscopynow.com/FCKeditor/UserFiles/File/specNOW/JMS36849.pdf

NIST Search of EI and MS/MS Databases at Eastman Chemical Company

tvasailor — Sun, 01 May 2011 15:08:54 +0000

This post summarizes some of the work we have done using the NIST search as our corporate system for searching and archiving our EI and MS/MS databases. It interfaces to many different manufacturer’s data processing systems and to a variety of structural drawing programs.

New Additions in Version 11 (2011): There was a recent update of the NIST library and some of the details are found in several excellent papers by David Sparkman:

http://www.icontact-archive.com/RFzlwXJu3LaBLbsYimXwZktKznO1HzqB?w=4

http://www.sepscience.com/emails/MSSol12NA.pdf?utm_source=iContact&utm_medium=email&utm_campaign=MS%20Solutions%20-%20North%20America&utm_content

Other details concerning new additions and purchase options can be found at SIS’s website:

http://www.sisweb.com/software/ms/nist.htm

Automatic Updating of Database Nightly at Eastman:

We add new EI and MS/MS spectra with structures to the database daily. The data base can be searched by mass spectrum, name, MF, MW, structure, etc. The following document gives details of the process for our automatic nightly update:

http://www.littledomain.com/james/files/nightly_update.pdf

To make this work will probably need the following utilities:

http://www.littledomain.com/james/files/ms_utilities.zip

Interfacing to Manufacturers’ Data Processing and Drawing Programs:

As I mentioned above, the program can be easily interfaced to an instrument manufacturer’s data system. I have included below a simple descripition that I wrote and a more detailed one from David Sparkman, a NIST consultant.

http://www.littledomain.com/james/files/simple.pdf

http://www.littledomain.com/james/files/detailed.pdf

We use the NIST search with a variety of data processing programs including Xcalibur, WSearch, AMDIS, MassLynx, Agilent MassHunter, and Agilent MSD and with a variety of structural drawing packages. Here is a link for more information on utilizing the NIST search with these other programs:

http://littlemsandsailing.wordpress.com/2011/08/28/using-nist-search-program-with-data-processing-and-drawing-programs/

Eastman Manual for Using NIST Search:

NIST has manuals for both AMDIS and the NIST Search. In addition, I wrote a manual for using the NIST search software for our Eastman users:

http://www.littledomain.com/james/files/users_manual.pdf

Illustrious History of NIST Library:

David Sparkman wrote a history of the NIST Library in Separation Science.

http://www.sepscience.com/emails/MSSol11NA.pdf?utm_source=iContact&utm_medium=email&utm_campaign=MS%20Solutions%20-%20North%20America&utm_content

List of Publications and Patents

tvasailor — Sun, 01 May 2011 14:46:48 +0000

Identification of “known unknowns” utilizing accurate mass data and chemical abstracts service databases
By Little James L; Cleven Curtis D; Brown Stacy D
From Journal of the American Society for Mass Spectrometry (2011), 22(2), 348-59.

Preparation of polyester samples for composition analysis
By Tindall, G. William; Perry, Randall L.; Little, James L.; Spaugh, Arthur T., Jr.
From Analytical Chemistry (1991), 63(13), 1251-6.

“Deuterated Ammonia Chemical Ionization: Use in Counting Exchangeable Hydrogen Sites on Organic Compounds,” A. Z Kamzelski, J. L. Little

From The Encyclopedia of Mass Spectrometry, Volume 4, Fundamentals of and Applications to Organic (and Organometallic) Compounds, Edited by M Gross et al, p 772-780, D. M Parees, 2005.

Artifacts in trimethylsilyl derivatization reactions and ways to avoid them, J. L. Little

From J Chromatogr A. 1999 Jun 4;844(1-2):1-22.

Liquid chromatography-mass spectrometry/mass spectrometry method development for drug metabolism studies: Examining lipid matrix ionization effects in plasma
By Little, James L.; Wempe, Michael F.; Buchanan, Charles M.
From Journal of Chromatography, B: Analytical Technologies in the Biomedical and Life Sciences (2006), 833(2), 219-230.

Building new drug delivery systems: in vitro and in vivo studies of drug-hydroxybutenyl cyclodextrin complexes
By Buchanan, Charles M.; Buchanan, Norma L.; Edgar, Kevin J.; Klein, Sandra; Little, James L.; Ramsey, Michael G.; Ruble, Karen M.; Wacher, Vincent J.; Wempe, Michael F.
From ACS Symposium Series (2009), 1017(Polysaccharide Materials), 31-64.

Inhibiting efflux with novel non-ionic surfactants: Rational design based on vitamin E TPGS
By Wempe, Michael F.; Wright, Charles; Little, James L.; Lightner, Janet W.; Large, Shannon E.; Caflisch, George B.; Buchanan, Charles M.; Rice, Peter J.; Wacher, Vincent J.; Ruble, Karen M.; et al
From International Journal of Pharmaceutics (2009), 370(1-2), 93-102.

Pharmacokinetics of Saquinavir After Intravenous and Oral Dosing of Saquinavir: Hydroxybutenyl-β-Cyclodextrin Formulations
By Buchanan, Charles M.; Buchanan, Norma L.; Edgar, Kevin J.; Little, James L.; Ramsey, Michael G.; Ruble, Karen M.; Wacher, Vincent J.; Wempe, Michael F.
From Biomacromolecules (2008), 9(1), 305-313.

Pharmacokinetics of itraconazole after intravenous and oral dosing of itraconazole-cyclodextrin formulations
By Buchanan, Charles M.; Buchanan, Norma L.; Edgar, Kevin J.; Klein, Sandra; Little, James L.; Ramsey, Michael G.; Ruble, Karen M.; Wacher, Vincent J.; Wempe, Michael F.
From Journal of Pharmaceutical Sciences (2007), 96(11), 3100-3116.

A Short and Convenient Chemical Route to Optically Pure 2-Methyl Chromanmethanols. Total Asymmetric Synthesis of β-, γ-, and δ-Tocotrienols
By Couladouros, Elias A.; Moutsos, Vassilios I.; Lampropoulou, Maria; Little, James L.; Hyatt, John A.
From Journal of Organic Chemistry (2007), 72(18), 6735-6741.

Pharmacokinetics of tamoxifen after intravenous and oral dosing of tamoxifen-hydroxybutenyl-β-cyclodextrin formulations
By Buchanan, Charles M.; Buchanan, Norma L.; Edgar, Kevin J.; Little, James L.; Malcolm, Michael O.; Ruble, Karen M.; Wacher, Vincent J.; Wempe, Michael F.
From Journal of Pharmaceutical Sciences (2007), 96(3), 644-660.

Characterization of ‘Schizokinen’, a dihydroxamate-type siderophore produced by Rhizobium leguminosarum IARI 917
By Storey, E. P.; Boghozian, R.; Little, James L.; Lowman, Douglas W.; Chakraborty, R.
From BioMetals (2006), 19(6), 637-649.

On the preparation of carbohydrate sulfates by displacement of trifluoromethanesulfonates
By Hyatt, John A.; Little, James L.
From Carbohydrate Research (1991), 220, 215-17.

α-D-Cellooligosaccharide acetates: physical and spectroscopic characterization and evaluation as models for cellulose triacetate
By Buchanan, Charles M.; Hyatt, John A.; Kelley, Stephen S.; Little, James L.
From Macromolecules (1990), 23(16), 3747-55.

Characterization of ‘Schizokinen’; a dihydroxamate-type siderophore produced by Rhizobium leguminosarum IARI 917
By Storey E P; Boghozian R; Little James L; Lowman Douglas W; Chakraborty R
From Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine (2006), 19(6), 637-49.

Light absorbing compositions useful for marking or tagging articles for security identification
By Pearson, Jason Clay; Weaver, Max Allen; Dawsey, Timothy Ray; King, Greg Alan; Clark, Mark Dwight; Little, James Lon; Schick, Martin Frederick
From U.S. Pat. Appl. Publ. (2007), US 20070287822 A1 20071213.

Marix Effects in LC-MS: Simple Way to Monitor

tvasailor — Sun, 01 May 2011 14:27:31 +0000

This post shares information on our work in the area of matrix effects. Matrix effects in LCMS can affect sensitivity, precision and accuracy. We have developed a simple way to monitor phospholipids and lysophospholipids which yield matrix effects. This approach is easily used in developing MRM LC-MS-MS analyses.

I have attached several links on the internet including:

ASMS Poster Sessions:

http://littledomain.com/james/files/matrix_part1.pdf

http://littledomain.com/james/files/matrix_part2.pdf

Prepress of Journal Article:

http://littledomain.com/james/files/text.pdf

A published copy of the article can be found at J. L. Little, M. F. Wempe, C. M. Buchanan, Journal of Chromatography B, 833 (2006) 219-230.

Preparation of polyester samples for composition analysis

tvasailor — Sun, 01 May 2011 14:10:48 +0000

This post shows the reference in Analytical Chemistry of a method we find very useful in our laboratory for the identification of polyesters and the quantitation of their monomer compositions. I don’t have a reprint or prepress for this article, so you would have to order a copy.

Preparation of polyester samples for composition analysis
By: Tindall, G. William; Perry, Randall L.; Little, James L.; Spaugh, Arthur T., Jr.
Analytical Chemistry (1991), 63(13), 1251-6.

http://pubs.acs.org/doi/abs/10.1021/ac00013a013

Abstract: A mixture of hydroxide, MeOH (methanol), and DMSO (dimethyl sulfoxide) solvolyzes polyesters at rates much faster than any reagent previously described for hydrolysis to monomers prior to analysis. Even highly crystalline polyesters can be solvolyzed to their corresponding monomers in a few minutes with this reagent. Three methods for the analysis of polyesters are described that use this reagent for the rapid preparation of the polymer sample. Methods for the determination of acids, diethylene glycol in poly(ethylene terephthalate), and glycols and diacids by NMR (nuclear magnetic resonance) are described. The reagent can be used to prepare samples for analysis by chromatography or NMR.