Thank you for this very informative video Mr. Little! I am currently teaching myself to analyze GC-MS data as there is nobody available to teach me. Your webinar series is an invaluable resource to that end!
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.
Thank you so much for this video. I am learning this on my own at work, so it has been a slow process, but this video showed me a lot of things I was unaware of in this software. Question: Is there a way to subtract a baseline/constant? One of my GC columns was contaminated with a silicone oil, so the output looked great with the exception of about 4 masses that were ever present. While that is fixed now (though the new column has fewer theoretical plates) my helium supply is contaminated with a bit of argon, and it would be nice to just ignore that line. Thanks again for the work you did for this presentation.
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!
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!
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
My another doubt is, NIST shows compounds like Formic acid, 2-ethylhexyl ester... so is it Formic acid only with some additional compound during derivatization or the whole is the main compound
Hi James, I am working on LC-MS/MS for phenolic metabolites, is this library will be useful or you have any suggestion how to process MS/MS data through library. Thnaks
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 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.
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.
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Thank you for this very informative video Mr. Little! I am currently teaching myself to analyze GC-MS data as there is nobody available to teach me. Your webinar series is an invaluable resource to that end!
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.
Thank you so much for this video. I am learning this on my own at work, so it has been a slow process, but this video showed me a lot of things I was unaware of in this software.
Question: Is there a way to subtract a baseline/constant? One of my GC columns was contaminated with a silicone oil, so the output looked great with the exception of about 4 masses that were ever present. While that is fixed now (though the new column has fewer theoretical plates) my helium supply is contaminated with a bit of argon, and it would be nice to just ignore that line.
Thanks again for the work you did for this presentation.
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!
Hi Dr. James, I need to know about the already derivatized sample, most of the search results appear with TMS, so the main compound is before the tms
you just have to take off the TMS to get structure of original compound
how do you paste in in peak lists? (sorry in advance if this is covered later than where I am)
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
My another doubt is, NIST shows compounds like Formic acid, 2-ethylhexyl ester... so is it Formic acid only with some additional compound during derivatization or the whole is the main compound
if 2-ethylhexyl ester, that is what it is, not the alcohol or free formic acid
Really useful video to get the hang of this software, thanks!
Glad it was helpful!
glad it is helping, lots of things on my website related
littlemsandsailing.com/
One small question: How come that you use MS Search 2.4 when the official versions are called 2.0f or 2.0g?
I am using the newest version of MS Search delivered with NIST20 library, some differences over the versions that you refer to
Hi James, I am working on LC-MS/MS for phenolic metabolites, is this library will be useful or you have any suggestion how to process MS/MS data through library.
Thnaks
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
Can u describe a result of gcms for me as I cannot understand it
gcms is used to identify organic compounds in a mixture
I have two results as of aqueous and methanolic extract of plant sample
no worries, just analyzed by gcms as derivatized forming TMS derivative or possibly underivatized
Thank you very much.
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
Can you send me link for download this program free? Please
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
Thank you so much, too useful. But need how can install it
look on NIST for free version to download or buy the library from a distributor and comes with install disk for software