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your welcome

your welcom..

@jameslittle2264 please if have Angilents LC MSMS .i would like to learn from video.

@@amornratrat see littlemsandsailing.com/2024/10/using-agilent-masshunter-to-perform-nist-msms-search/

Glad it was helpful!

Fred McLafferty's book on interpretation is what i started with many years agoa

Sounds like some problem when installing the NIST search program. Might uninstall all the NIST software and try again. Usually the NIST search software and AMDIS will be present at the same level in the NIST23 folder, e.g, NIST23/AMDIS/AMDIS_32.exe and NIST23/MSSearch/nistms.exe, NIST technical support is very good by contacting David Sparkman <ods@compuserve.com>

Thank you so much for your reply. Will check that out.

@@laplynnchua683 also remember than you must first run the deconvolution program before you are able to send a spectrum to manual nist search, always thought that was somewhat counterintuitive, but apparently not to the nist programmers..

littlemsandsailing.com/2020/08/ms-master-class/ Part IV

you use AMDIS to get spectra into the speclist for searching. Other programs from Agilent and Thermo will send their spectra to speclist for searching. The user can also add their spectra manually peak by peak in the librarian tab entering the basepeak as 100 or 1000 intensity and then all the other peaks the appropriate intensity relative to the base peak. Manually is not recommeded, very time consuming. AMDIS processes the files of many different instrument manufactures, you just have to know where the file is located and specify the correct file format in AMDIS. I also have a simpler course which includes free spectra and software that I developed for university students, littlemsandsailing.com/2023/08/university-laboratory-for-gcms-data-processing/ Good luck and fair winds!

@@jameslittle2264 so there is no way to copy a peak/intensity list? What about using the MS interpreter program?

nope, can create an msp file and import it, can see the MSP format in their manual or take one of their library spectra and export in MSP format. MSP contains some meta data such as name, MF, MW, but the main thing is for the msp file to tell the number of m/z pairs in the file which is then listing the m/z vs intensity files. Essentially AMDIS, Thermo, and Agilent create that MSP file for you when you send a spectrum to the NIST search from the these programs

the AMDIS manual shows you how to look for targeted comopunds if you make a library containing the species of interest, when AMDIS finds, will mark with a T, don't think I demonstrated that in any of my videos, but the AMDIS manual does that, a simpler way is to just plot ions of interest in the unknown spectrum that are somewhat unique and see their extracted ion chromatogram versus time in AMDIS

​@@jameslittle2264 yes, you have mentioned in one of your videos about T mark against "targets" in your spectrum. I'm interested in knowing how I can add compounds of interest in a library if I DON'T have their spectra?. I have made my own library but it contains compounds whose spectra I already have from my GCMS data. There's this NIST Chemistry webbook where I can look at a spectrum of compounds of my choice, but it's not downloadable.

@@afifalaraib9159 I have copies of the NIST and Wiley and other libraries, about 1.7 million EI spectra plus I get 14,000 each year from NIST for quality evaluation and also new ones from Wiley. Thus maybe at least buy the newest NIST and Wiley in NIST format and can save the spectrum of interest in MSP format and use add to AMDIS library for T (targeting) or as a minium plot extracted ion chromatograms in AMDIS to look for things of interest. If not exact spectrum in Wiley or NIST, can do similarity structure search to guess what your spectrum might look like and then plot the appropriate ion in AMDIS. Normally I search everything in the file of interest noting what is certain and use that information to refelect on possible identities of unknowns. Accurate mass and CI is very important for unknown identification. As you can see, an involved process and a variety of approaches including sample history involved in unknown identification.

@@jameslittle2264 thank you very much for your insights. It helped a lot. And thank you for the videos.

You should be able to go to Search Tab and search to see all the spectra in your library to make sure they were created. Also would need to make sure your libraries are indexed under the tools tab. In particular, InChikey, Structure, hybrid search if doing hybrid searches. Then make sure under library search options, make sure your library is selected in both the spectrum and structure searches. Hope this helps.

@@jameslittle2264 thank u for your help. One more question: under library search options, should I select RI (GC) option?

only if you have RI data on your compound that you measured with an RI ladder (mix of hydrocarbon standards), separate section on doing that with AMDIS

@@jameslittle2264 got it. I have added 3 libraries in Nist, one of my own & 2 are MONA libraries(GC & LC MS). I am not getting any hits of my spectra, even the ones which I added in my library (along with their structures). I have followed all the steps & guidelines that you mentioned

@@jameslittle2264 thank u. one more question: i have successfully added 3 libraries in NIST, one of my own and two from MONA (GC and LC MS). But i am not getting any hits from them, even from the spectra that I have added (along with relevant structures) in my library. How can i resolve this?

your welcome

cannot do with MS interpreter unfortunately

AMDIS should remove all these peaks when you deconvolute in NIST software. In Wiley KnowItAll, MSExpert should also removed. Can do manual background subtract in AMDIS, but it is not trivial. In KnowItAll, ProcessIt has a very good manual background subtract. Hope this helps! Fair winds and following seas!

Your welcome. See my website for more MS information. littlemsandsailing.com/

Good luck. See my website for other resources littlemsandsailing.com/ Also a simple NIST course with first link, or more detailed with second littlemsandsailing.com/2023/08/university-laboratory-for-gcms-data-processing/ littlemsandsailing.com/2020/08/ms-master-class/

the best way is to import from AMDIS, or Agilent, or Thermo software. Can enter in librarian one peak at a time, or if you have such a list put it in NIST MSP format and import it into the NIST search program. The MSP format has fields such as MW, MF, etc, but most important is the number of mass/intensity peaks in the list. I think their format is included in the NIST maual or a few such files are supplied with the software.

version 3, buy, old version free, littlemsandsailing.com/2023/08/28/university-laboratory-for-gcms-data-processing/

Quite a compliment from an expert such as you! Keep up all the great work in GCMS at Eastman.

Hope you find it useful, developed for a local friend, decided to share with others.

hope it is useful, good for free software!

at one time used MassHunter, but no longer, I know masshunter can send spectra to NIST search, but don't know if RI is one of the fields they send. You would have to try then look in the library editor/edit then either the additional info or experimental data fields or see if they populate the correct RI field when sending to NIST search.

ruclips.net/video/Gi-SOJmMJVM/видео.html

your welcom

if 2-ethylhexyl ester, that is what it is, not the alcohol or free formic acid

you just have to take off the TMS to get structure of original compound

thanks

your welcome

no worries, just analyzed by gcms as derivatized forming TMS derivative or possibly underivatized

gcms is used to identify organic compounds in a mixture

Thanks for the feedback

Don’t know besides reloading

No you cannot do with MS interpreter

Glad it was helpful!

depends on which software one uses and which libraries are available, can try the NIST MSMS library which is the largest using the video course that I teach on MSMS spectra, wiley has MSMS library but much smaller and there is the MONA library. I don't know which would be the best for your app, would have to try, if use something like mass hunter, the software can import accurate mass data into the NIST hybrid search

@@jameslittle2264 hi james, I have MASS hunter. Can you share link from where I can't download MS/MS library.

@@jameslittle2264 I am using MS dial for MS/MS data analysis. If You will me to provide NIST MS/MS library, it will be grateful for me. Thanks for reply.

@@selenophileselenophile7289 in nist format drive.google.com/file/d/1yfuYVN62liLmj8JQiKi_25EPf4dmFyhX/view

look on my website, whole course on NIST and LCMS

Many thanks!

your welcom

Glad it was helpful!

glad it is helping, lots of things on my website related littlemsandsailing.com/

your most welcome

look on NIST for free version to download or buy the library from a distributor and comes with install disk for software

came with my version of NIST 20 library, so free in a sense because not charged for the search software

free download of software on nist website, but must pay for library

I am using the newest version of MS Search delivered with NIST20 library, some differences over the versions that you refer to

Thanks

Now I am using GC-MS-SPME develop method off-aroma in milk powder. Qualitative check RT and m/z from nist with mix standards aldehydes such as propanal ,butanal ,hexanal..... decanal . But I have problem propanal& butanal seems that mass not unique . These are not linearity. Do you have introduce to me?. I try concentrate 0.2-10 ppb.sorry my English is not very good.

propanal m/z 58 and butanal (m/z 72) do have different spectra, take a look in the nist library