Hi very good video. Thank you. I get a problem when I right click on spectrum to do a mass spectrum search using nist ms program . The nist pathway does not show up. I am unable to locate the nist ms directory. Can you suggest how I can resolve this ?
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
@@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..
a question: how can I check the presence of certain compounds(from their MOL or SDF files) in my GCMS data in AMDIS? One solution that comes to my mind is to convert the structures in .msp format & then run through my GC MS data. But how can I achieve this ?
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.
Thank you for video, it is very helpful
Glad it was helpful!
Hi very good video. Thank you. I get a problem when I right click on spectrum to do a mass spectrum search using nist ms program . The nist pathway does not show up. I am unable to locate the nist ms directory. Can you suggest how I can resolve this ?
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
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..
a question: how can I check the presence of certain compounds(from their MOL or SDF files) in my GCMS data in AMDIS? One solution that comes to my mind is to convert the structures in .msp format & then run through my GC MS data. But how can I achieve this ?
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.