Posted by: tvasailor | May 24, 2012

Overview “Known Unknowns”

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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:

flowchart3

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

or the direct link to the Chromatography Online Website:

LCGC Article On-Line Link

which can be printed using the instructions in this link.  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:

types_of_databases_searches
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:

nist_search

“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 | August 3, 2015

Useful Tips for 1D and 2D NMR Experiments

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NMR

I have primarily done mass spectrometry during my career, but also utilize NMR data in conjunction with mass spectrometry data to identify components.  Often even relatively complex mixtures can be characterized by 1D and 2D NMR data utilizing complimentary information obtained by either LC-MS or GC-MS analyses.

Laura Adduci shared with me a very useful NMR presentation of tips, tricks, and techniques.  Laura currently works in our NMR laboratory at Eastman Chemical Co., but prepared the presentation while attending UNC-Chapel Hill.

NMR at UNC:  Tips, Tricks, and Techniques

We also utilize both carbon and proton NMR for quantitative analyses.  It is a very powerful approach because standards are not required to calibrate the instrument response.  All that is required is that the component or components of interest be correctly identified.  I have included three links below that I have found very useful for quantitative NMR analyses:

Practical Guide for Quantitative 1D NMR Integration

Practical Aspects of Quantitative NMR Experiments 

Quantitative 1H NMR

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Posted by: tvasailor | March 17, 2015

Archives of Old Articles and Mass Spec Documentation

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raiders_of_the_lost_archive_450
ASMS History Site:  The American Society for Mass Spectrometry has a great site managed by ASMS member/archivist, Michael Grayson.

ASMS History Site

CHF HIstory Site:   Also, great information at the Chemical Heritage Foundation site.

CHF History Site

BMSS History Site:  A new history site for the British Mass Spectrometry Society site.

BMSS History Site

Historical Documents from My Archives:  I found many mass spec artifacts when cleaning out my office in anticipation of retirement in early 2016.  My wife warned me their wasn’t unlimited room in our house or on our sailboat for lots of things.  Thus, I began to sort through and discard things in my office at Eastman and post ones of general interest on my website.

Finnigan Corporation:  A lot of my early career was greatly influenced by GC-MS software (INCOS) and hardware (chemical ionization) from the Finnigan Corporation.  Thus, many of the items on this archive page originated from Finnigan.

I was love stricken in my first encounter with our Finnigan 4000 series instrument and my love affair continued with the TSQ, DSQ, and ISQ instruments.  But possibly the first love was the best.  The Finnigan 4000 was a phenomenal piece of technology, software and hardware, for her time.  We routinely ran the instrument 24/7 using automated acquisition and automated data processing for both qualitative and quantitative analyses.

finnigan_4000

I found several articles about Robert E. Finnigan on the internet that I found interesting inlcuding a short biography and a long interview.

Robert Finnigan short biography
Robert Finnigan long inverview

Finnigan Cookbook, 1979:  This is the Finnigan Cookbook given to me by Bill Tindall, a retiree from Eastman Chemical Company.  It had the following documentation on the front page:

“Marcie got the recipe and passed it to Mark Weiss of Finnigan-INCOS.  Mark Weiss compiled it into his now famous cookbook using what is now considered the first word process software which was written by Joel at INCOS.  The cookbook was printed from the Stanford computer Christmas day in 1979, copied at Finnigan during the dark of night and distributed to its contributors who were acknowledged only by their street names.  For all that its not a bad recipe.”

I made only a few changes when scanning the document.  I did character recognition and added title pages between sections because the handwritten ones could not be scanned.

Finnigan Spectra Vol 6 No 1 (1976):  I always enjoyed the early Finnigan Newsletters.  This newsletter contained the following very useful article which we utilized the work of Hunt on our Finnigan 4000/4500 in 1979 in the analyses of photographic chemicals for Kodak:

-Selective Reagents for Chemical Ionization Mass Spectrometry, Don Hunt, University of Virginia
-Application of Gas Chromatography-Chemical Ionization Mass Spectrometry to the Analysis of Microquantities of Choline and Its Esters, Israel Hanin, University of Pittsburgh School of Medicine

Finnigan Spectra Vol 2 No 1 1972:  Another old Finnigan Newsletter containing articles with articles by M. S. Story and R. E. Finnigan and other things.

Chemical Ionization Mass Spectrometry, E. J. Bonelli, M. S. Story
Analysis of a Kraft Paper Mill Effluent by Electron Impact and Chemical Ionization GC/MS, J. B. Knight, E. J. Bonelli, and R. E. Finnigan
GC/MS of Chlorinated Dioxins, E. J. Bonelli
Dateline:  Finnigan acquires Quanta/Metrix

Finnigan Spectra Vol 12 No 1, Spring 1989:  A collection of early LC-MS articles in a Finnigan magazine.

Letter to the Reader, Richard M. Caprioli
Continuous Flow Fab, Richard M. Caprioli
Capillary Zone Electrophoresis/Mass Spectrometry:  An Alternative to LC/MS?, Richard D. Smith, Charles J. Barinaga, and Harold R Udsetb
Supercritical Fluid Chromatogrpahy/Mass SPectrometry (SFC/MS), D. E. Games, A. J. Berry, S. Y. Hughes, S. Mahatheeranont, I. C. Mylchrest, J. R. Perkins, E. D. Ramsey, and S. Pleasance
Thermospray LC/MS:  Effect of Experimental Parameters on Spectra and Sensitivity, Patrick J. Rudewicz
Perspectives on the Moving Belt LC/MS Interface, J. van der Greef, W. M. A. Niessen, and U. R. Tjaden

Finnigan Spectra Vol 9 No 1 Spring 1983:  Another collection of early LC-MS articles, listed Finnigan thermospray interface.  The Thermospray interface is the first useful interface utilized at Eastman Chemical Company.  We utilized the Vestec interface on our Finnigan 4000/4500 GC-MS.  We tried a moving belt interface on a contract instrument in Boston, but we were not impressed, and thus, never purchased one.

Introduction, D. E. Games, guest editor
Combined Liquid Chromatography/Mass Spectrometry (LC/MS), D. E. Games
The Moving Belt as an Interface for HPLC/MS-P. Vouros, B. L. Karger
First Steps in LC/MS with Simple Interfaces for the Finnigan MAT 44-N. Evans
Experiments with the Coupling of a Jasco Micro LC to a Finnigan MAT 3300 Quadrupole Mass Spectrometer, A. P. Bruins, B. F. H Drenth
Thermospray LC/MS:  Supplement of Substitute for Existing Techniques, W. H. McFadden

Finnigan Application Report Number AR8020, 1979?:  We found negative ion LC-MS to be really useful for Thermospray and later electrospray analyses.  We did some negative ion GC-MS, but not as universally useful.  Here is an early report on negative ion MS from Finnigan:

Biomedical Applications of Negative Ion Chemical Ionization Mass Spectrometry, John R. B. Slayback and M. N. Kan, Finnigan Corporation

Finnigan Application Report No 47, 1982?:  We did a lot of direct chemical ionization on both our Finnigan 4000/4500, Finnigan 700/7000, and even our Autospec.  Worked reasonably well before the days of electrospray.  We normally would isolate compounds by preparative TLC or flash chromatography.

DCI-Direct Chemical Ionization or Desorption Chemical Ionization, A Powerful Soft Ionization Technique in Mass Spectrometry, U. Rapp, G. Meyerhoff, and G. Dielmann

Finnigan Technical Report No TR8027:  I loved my first GC-MS instrument, a Finnigan 4000 and its associated Data General computer, analytical-digital interface, jet separator, chemical ionization source, oscillope for tuning, library search software, etc.  Here is the information needed to optimizie the INCOS data system.

Optimization of Acquisition Parameters for the INCOS Data System, Rhilip L. Warren, John R. B. Slayback, Carl R. Phillips

Finnigan TSQ70-We had a Finnigan TSQ-70 and two SSQ-70’s.  We really enjoyed all three instruments doing a lot of chemical ionization work, Vestec thermospray interface, Vestec particle bean interface, fast atom bombardment interface, and direct chemical ionization.  Here is a picture that Steve Lammert shared with me recently.  It is of the  TSQ 70 development team photo ca. 1985.

tsq70

Direct Liquid Introduction (DLI) LC-MS Interface, 1984:  Jack Henion came to our lab to install the DLI interface.  He was a consultant for Kodak in Rochester.  Many people referred to it as “Pray and Spray” because always plugging.  Here is some documentation and data I retained even the parts listing for the various laser drilled holes.  We only used a very short time before transitioning to the Thermospray interface.

Vestec Particle Beam Interface Brochure:  We used this for several years in both EI and CI modes on our Finnigan TSQ-700.  It actually worked well, but the sensitivity was very poor compared to current electrospray interfaces.  Nevertheless, one could get good EI spectra for library searching and addition to our computer searchable Eastman Corporate Database.

Additional Particle Beam Information:  I have included some additional data on the Vestec interface, the Hewlett-Packard demo, the Extrel Thermabeam interface, and the Particle Beam/FAB interface custom-built by Marvin Vestal for our VG-70 MS,  etc.

Kodak Laboratory Chemicals Bulletin Vol 55, No 3, 1984:  When I was in graduate school in the late 70’s, we ordered specialty chemicals from Kodak.  They supplied many in that era, but nothing to compare to the large list of chemicals from Aldrich.  Here is a bulleting talking about “The Chemistry of the Diketene-Acetone Adduct” by Robert J. Clemens, CAS No. 5394-63-8, 2,2,6-trimethyl-4H-1,3-dioxin-4-one.

MS9 Design Lectures, AEI, Associated Electrical Industries Limited:  I think we had a MS9 in the Kodak Rochester laboratories.  We did have a CEC 21-110B mass spectroemeter in Research at Eastman Chemical.  We used the instrument at Eastman to characterize TLC fractions, prepared samples, and even components trapped off a GC/TCD system.  Thus the beginnings of GC-MS!

Finnigan 1015 GC-MS:  We had one of these systems at Eastman.  Bob Finnigan would always ask me about it every year when I attended ASMS in the mid 80’s.  The picture below was from the Heritage article written by David C. Brock.  I think I would have remembered that lady if she had worked in our lab..

finnigan 1015 picture

INCOS 50:  We had one of these systems.  It always looked to me as if someone had made the manifold for the system produced from a “glass sewer pipe.”  Probably the best part of the instrument was the INCOS library search software:

S. Sokolow, J. Karnofsky, P. Gustafson, The Finnigan Library Search Program, Finnigan Application Report 2, San Jose, CA (1978).

A good friend of mine supplied me a copy of the report.

Here is a link to an ACS advertisement for the instrument featuring Bob Finnigan.

incos 50

British Mass Spectrometry History:  One of my wife’s British relatives, Winifred Hall, was a early scientist in mass spectrometry at Shell.  When we went to visit her, she introduced me to several people in the mass spectrometry industry including Robert Craig.  Robert was an early founder of VG.

This was actually before my career in mass spectrometrist at Eastman Kodak.  At the time, I was attending the University of Georgia as a graduate student in chemistry, but our school did not have a working mass spectrometer.  It had been “hit” by lightening and no one knew how to repair the beast!

I found a lot of history of the British mass spectrometry community on the British Mass Spectrometry website that is very interesting.

Mike Morris – 50 years of British MS

BMSS 50th poster by ASMS

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Posted by: tvasailor | July 11, 2014

Accurate Mass User Libraries in NIST14 Release

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Users can now add accurate mass EI and MS/MS to their libraries.  This is an updated feature distributed with the recent NIST 14 library and Search software release.  A brochure from a distributor is shown below and also another link to “What’s New”:

NIST Brochure

“What’s New NIST14”

I have shown some examples of accurate mass EI and MS/MS spectra in the following link:

Examples User Accurate Mass EI and MS/MS Spectra in NIST14 Software

acc mass

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Posted by: tvasailor | June 20, 2014

University of Georgia Graduate Work 1978

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My thesis at the University of Georgia was supported by federal grant money to develop solar energy.  It was based on the “Evaluation of Heterogenous Photosensitizers.”  The solid state sensitizers were used to store energy by the conversion of  norbornadiene to quadricyclane.  The quadricyclane can then be converted quantitatively back to norbornadiene to recover the energy in the form of heat.

Thesis Link

solar_energy

I have also included my graduate Seminar on “Brevicomin:  Structure and Synthesis of a Novel Natural Product.”

Brevicomin Link

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Posted by: tvasailor | July 5, 2013

File Conversions and Data Intechange

File Conversions and Data Interchange

Eastman supported the early efforts in netCDF/Andi.  It has always been very important for our users to be able to convert files from one vendor’s format to another.  Often one software package will have capabilities that another doesn’t possess or someone might only have training in one software package and not another.  We served on ASTM committees and also we required vendors to supply the format as part of instrument purchases.

These capabilites have been critical to our operations since those early days and they are still employed daily!  Our early work was discussed briefly in one of the Andi Newsletters in 1995.

We currently use file conversions daily.  We primarily convert files obtained on our Thermo DSQ GC-MS systems to netCDF format using Thermo’s  File Converter program.

thermo_file_converter

The resulting netCDF files are then converted with Water’s DataBridge program for processing with Water’s MassLynx software package.

waters_file_converter

In addition, we use MassTransit which is a legacy product still distributed by Scientific Instrument Services Company.  It is used primarily for converting files to and from our Agilent GC-MSD instruments to other vendor formats.

mass_transit

Scientific Instrument services also sells another translator package called GC/MS File Translator, but we have not used that program.

Dr. Philip Winig (see his comments below) sent me a note about OpenChrom software.  It is open source software for chromatography and mass spectrometry based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively, but also performs files conversions.  I haven’t had the opportunity to evaluate the software.

Posted by: tvasailor | December 30, 2012

“Known Unknown” Future Improvements Needed

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Our 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.  I have discussed some of my thoughts and opinions below and a good review of small molecule identification was recently published.

1.  CAS Registry/SciFinder:  The major improvement needed in SciFinder is the addition to search by monoisotopic mass within a specified m/z error window.  This would be especially useful for higher molecular weight components, but could be used effectively for all components eliminating the need for any subjective decisions in specifiying the elements searched, numbers of double bond equivalents, numbers of elements, etc. in the determination of a molecular formula.  The resulting structures from the monoisotopic searches could be returned to the manufacturers’ software and further ranked/sorted by their isotopic fidelity and mass error.

Recently, CAS did add the ability to search by average molecular weight in SciFinder.  This capability was only previously available in STN Express.  This is useful, but the monoisotopic mass can be determined with much better precision and accuracy than the average molecular weight.  At lower m/z values too many candidates are recovered due to the very large number of components in the CAS Registry between 300-500 daltons and the large measurement error.

ChemSpider has an applications program interface (API) which can be used by manufacturers to query the ChemSpider database and return results to their interfaces for further processing/displaying.  A similar type approach would be very useful for the CAS Registry.  The Registry does currently allow one to manually export a reasonable number mol files (structural connection tables) in an SDF file format.  It would be very desirable to also included other fields in the SDF file such as the number of associated references.

Other needed improvements (limitations) are found on page 12 of a prepress article found on this website.

2.  Chemspider:  There are many duplicate structures in ChemSpider for the same compound.  CAS Registry does a better job of listing a unique structure for each record.  Several other suggestions for ChemSpider are found on page 8 of a prepress article.

3.  In-Silico Fragmentation:  Many programs exist for the in-silico fragmentation of structures including MS Interpreter (NIST), MetFrag, Molecular Structure Correlator (Agilent), MathSpec (D. Sweeney), and Fragmentation Prediction Tool in PeakView Software (AB Sciex).  Much more needs to be done in this area to improve the reliability of ranking candidate structures by comparison of in-silico spectra to acquired CID spectra.  A section in a review article discusses the current state of in silico work.

4.  Automated Processing and Reporting:  Manufacturers are improving their automatic processing and reporting for LC-MS and GC-MS, but we still spend an unacceptable amount of time hand-annotating chromatograms for customers.  Much of this could be avoided if manufacturers would further improve their software.

It would be very powerful if both ChemSpider and CAS Registry used application program interfaces to obtain structures and associated numbers of references which would be returned to the manufacturers’ software programs.  They could then be ranked by individual scores considering the number of associated references, isotopic fidelity, mass accuracy, isotopic spacing, elemental composition from fragmentation data, in-silico fragmentation, commercially availability, etc.  Then an overall score could be assigned by weighting these individual scores to allow sorting of the candidate structures.

Someday..

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Posted by: tvasailor | December 30, 2012

Identifying “Unknown Unknowns”

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There will be many non-targeted species found in environmental and commercial samples which are “unknown unknowns.”  In other words, compounds which are not found in any spectral databases or even large “spectra-less” databases such as the CAS Registry or ChemSpider.  These species are noted as yielding “No Results” in our process flowchart.

Many of the these will be “transformation products” formed by oxidation, dealkylation, hydrolysis, etc. of “known unknowns” identified in the sample of interest.   It is much more difficult to identify these components, but information obtained in the identification of other components in the sample will often yield information that facilitates their identification.

For example, many components will be metabolites formed from other components.  Thus software designed to identify metabolites by generating possible molecular formula from expected biotransformations will prove useful.  Furthermore, using the mass defect filter technique [1-3] to search for related compounds of identified components could be utilized.

In most of our commercial samples, “unknown unknowns” are routinely identified from common fragment ions and neutral losses noted for components identified in the sample.  With this data and accurate mass information, additional components can often be easily identified.  These newly identified components are then added to our in-house mass spectral/structural database for future reference.

References

1.  Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometry, J Mass Spectrom,  2009 Jul;44(7):999-1016. doi: 10.1002/jms.1610

2.  Metabolite Identification Using Multiple Mass Defect Filters and Higher Energy Collisional Dissociation on a Hybrid Mass Spectrometer, Spectroscopy 2008.

3.  Mass Defect Filtering:  a New Toot to Expedite Screening, Dereplication, and Identification of Natural Products, poster, XenoBiotic Laboratories Poster

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Posted by: tvasailor | December 28, 2012

CID (MS/MS) Libraries

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We routinely use both EI and CID (MS/MS) libraries to identify unknowns using the NIST MS Search.  The libraries employed include purchased commercial libraries and our in-house created libraries.  We do both spectral searches to identify compounds and structure searches to find model compounds.  Even if the component of interest is not in the library, spectral search results give valuable insight into substructural groups present in the structure of the unknown!

library_entries2

We can obtain nominal mass CID (collision induced dissociation), accurate mass CID (TOF), in-source CID (quad and TOF), and tandem CID spectra (QTOF, triple quad).  Below is an accurate mass QTOF spectrum obtained on our Agilent 6500 QTOF.

msms_spectrum

The following PDF file details information on creating and using in-house CID user libraries in NIST format:

Creating and Using_User_CID_Libraries

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Posted by: tvasailor | May 23, 2012

In Silico MS Fragmentation Data

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Eastman employs four different”in silico” software programs for processing MS/MS (CID) and EI spectra in our identification efforts.  The results are definitely not as useful as searching or examining experimentally acquired CID spectra.  Nevertheless, the use of in silico software programs and their associated spectra can definitely assist in shortening the time it takes to manually interpret and prioritize substructural information for candidate species.  In addition ABSciex has some interesting in silico capabilities and a section of a recent review article discusses the topic.

The software programs we use are listed below.

1.  Use of NIST MS Interpreter for EI and MS/MS Spectra

We routinely use NIST MS Interpreter to understand EI and MS/MS (APCI, electrospray) spectra.  It is critical part of entering compounds into both our EI and MS/MS libraries.  It quickly allows us to determine if all the major fragments in our spectrum are consistent with the proposed structure.  In addition, it can also be used to correlate fragment ions in a model compound’s spectrum to its substructure in the NIST and Wiley EI and MS/MS libraries and our in-house libraries.

ms_interpreter

It is supplied free of charge with the NIST Version 2.0 Software.  I have included screenshots of the MS Interpreter and a poster presented by NIST:

ms_interpreter_screenshots (2 pages)

ms_interpreter_NIST_poster

2.  MetFrag with SciFinder and ChemSpider

MetFrag looks very interesting.  It allows me to use an automated connection to ChemSpider and a manual connection to SciFinder to obtain candidate structures.  In silico CID spectra are generated for all the candidate structures which are then compared to my acquired accurate mass CID spectrum.  The best results appear to be obtained in my examples by sorting by the “# of Explained Peaks” instead of “Score” in many cases.

I have shown the results for the approach with both ChemSpider and SciFinder for trazodone:

trazodone_example

Their web links are:

MetFusion_link

MetFrag_link

If you want to try the trazodone example, the following link contains the mass spec data and the SDF file needed for the MetFrag query:

test_files_metfrag

3.  Identifying “Known Unknowns” Using ChemSpider and Automated MS/MS Structure Correlation

A poster session was given at the 2012 ASMS conference in Vancouver.  The work was done as a collaborative effort between Agilent, ChemSpider (RSC), and Eastman Chemical Company.  The approach is described below with a link to the poster session in PDF format:

  • Accurate mass data acquired by LC/MS in data-dependent MS/MS mode
  • Agilent MassHunter Qualitative Analysis software used to find compounds and generate molecular formulas using monoisotopic mass, isotope abundance, and isotope spacing, as well as look for matching formulas for each fragment ion and its neutral loss from the precursor
  • Prototype Agilent MassHunter Molecular Structure Correlator software uses ChemSpider interface to obtain candidate structures for a target molecular formula and associated number of references for candidate structures
  • Calculation of correlation scores to explain MS/MS fragmentation pattern for each candidate structure using a “systematic bond-breaking” approach
  • Results sorted by number of references and/or correlation score to evaluate structure candidates for identification of components

asms_2012_poster_agilent_chemspider

3.   MathSpec

MathSpec, Inc. is a privately held company based in the Chicago area. The founder, Dr. Daniel L. Sweeney, believes that mass spectral fragmentation data can best be interpreted by viewing small molecules as mathematical partitions of the molecular weight. Dan has been doing LC-MS and interpreting MS/MS data for over twenty years.

It seems to work well and he is also modifying to find similar compounds.  He added the capability to sort by number of associated synonyms which is similar to the concept of sorting by the number of references in other programs.

MathSpec_link

Also see his You Tube videos describing his new software including add-ins in Excel.  Just search with Google for “MathSpec You Tube.”

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