Hi,
Here are some things I have been struggling with, I hope someone can give some tips and tricks about my GC-MS data of essential oils.
Currently, I have agilent directories .D (and I don't have access to the chemstation software anymore so I really have to start from .D format).
I have been using the open-source tool openchrom to analyze the chromatograms and identify the compounds in my samples, by using MS data (just qualitative analysis). However, openchrom NIST search just does not work in my computer (either on windows and linux) and I could not solve the error together with the technical support. I was able to do something with a NIST demo library but it did not work also (and buying the full NIST library is not an option at the moment). I am able to convert the data to .cdf,.csv and .msp using openchrom (in case it is helpful).
Question1: Is there a tool to convert .D into a standard mass file (e.g. mzxml) for library search/to use in other pipeline? i tried proteowizard but it doesn´t recognize .D or the files .cdf,.csv and .msp converted with openchrom.
Additionaly, I was able to do manual ms search using massbank database (http://www.massbank.jp/) with csv files.
Question2: Is this database reliable for essential oils?
I would like to have at least 2 library results to support the identification.
Question3: Besides NIST, are there other reliable libraries for essential oils ms identification?
Question4: And what about open-source tools for ms identification (that actually work and the links are not dead) that can read .D or .cdf,.csv and .msp, other than openchrom?
Thanks in advance to any advice regarding any of the questions.
Pedro
I can't really help you with the conversion issues (1 and 4) - sorry. With regard to question 2 and 3: First of all, I would highly recommend to use retention indices. Mass spectra database search alone is not sufficient for identification, as some components, especially in the hydrocarbon monoterpenes and sesquiterpenes, are so similar that a distinction by mass spectrum only is almost impossible. The NIST is a good starting point and is quite reliable for common compounds (if RI are considered as well!), yet much less so in the sesquiterpenes and diterpenes. I can also recommend the software Massfinder 4 in combination with the Terpenoids Library (http://massfinder.com/wiki/Terpenoids_Library), or if you prefer the low-cost analog "version", buy the "Adams", a mass spectral library book focused on essential oils. I have worked with it and it is an excellent source, easy to use and includes over 2500 spectra (http://www.amazon.de/Identification-Essential-Components-Chromatography-Spectrometry/dp/1932633219/ref=asap_bc?ie=UTF8)
Hi,
1)
Since you have openchrom, you should be able to export to any other format or?
An alternative might be "trapper"
http://tools.proteomecenter.org/wiki/index.php?title=Software:trapper
2) Yes, to my knowledge. But incomplete (like the majority of Databases dealing with small molecules)
I would combine Wiley and NIST Databases
http://www.sisweb.com/software/ms/wiley.htm
3)
See 2)
4) not much here. I have a list for proteomics, but for metabolomics it is way more complicated.
You might want to check the Fiehn Lab at UC Davis
http://fiehnlab.ucdavis.edu/projects/identification
Alternatively, you can create a personal workflow with OpenMS
http://open-ms.sourceforge.net/
(Or search for one already published)
Elaborating on Johannes' reasoned response above: He is correct that we must use a "2-dimensional" approach that considers retention information and spectra for each peak. Retention is however you want to do it: time or index. Dr. Robert P. Adams is on ResearchGate and teaches at Baylor U in Texas. Yes his book is great, is exclusive to essential oils, we bought it, and every spectrum comes with the retention time for that compound. I contacted Dr. Adams this year and purchased the digital version of the library (TERPENES.L) and Agilent did a custom install for us. Now I double click on a peak and obtain the spectrum. Double click once more and I have the spectral matches ranked in order of match quality, with retention times. I would not waste precious money on purchasing NIST, though it is lots of good spectra, because NIST contains zero retention information for anything. If you want to purchase more than Adams' 2200 spectra you can spend 3 times as much and get a bigger database, by an Italian researcher, through Wiley publisher, that is also on essential oils and comes with retention info. Good luck on your project- have you asked Agilent for help? b/c they have great resources and since you are at University, this is opportunity for Agilent to train a cadre of young people who may then go out into the world and buy Agilent stuff! Also Dr. Adams compiled his database, beginning in 1977, on a Hewlett Packard instrument that is the direct predecessor of the Agilent GCMS. Much of the engineering is so similar. This makes the spectral match quality amazing- so if you have Agilent hardware, even more reason to go with Adams.
MassFinder is an excellent analysis tool and comes with a nice terpenoid database
Dr. Adams this year and purchased the digital version of the library (TERPENES.L) and Agilent did a custom install for us.
Are you using Agilent MSD ChemStation or MassHunter? You can set up a method for analysis in the separate data analysis software for peak integration and spectral identification. I have also used AMDIS (should be complementary if you have purchased a NIST library) and PBM Benchtop for data analysis. No conversion needed for these programs. If you know what compounds you are looking for, you can always add them manually to your mass spectral database after shooting your own pure standard. Good luck.
As read above, I also suggest Amdis32 from Nist. It is free and it can either read .d agilent format or .xml Mass Hunter Agilent data, but you cannot convert one to the other.
You may open an Agilent File xx.D, see the TIC and the various mass spec, perform background subtraction, peak deconvolution etc. However, to perform a full library search for peak identification, you must separately have the Nist MS search program on your system. Using Amdis32 alone, without MS search, you could build your own library from standards, but it is time consuming. GC/MS manufacturers sometimes install a proprietary GC/MS data system, and separately provide the full Nist MS search program, but do not necessarily install it on the computer. Check if MS search 2.0 is present, then using Amdis32, you may perform a complete qualitative analysis of your GC/MS data. Note that Amdis32 is only for qualitative analysis, and not for quantitative calculations.
Hello I'm from Texas Bio med and looking for open format data analysis software and how it work for biological sample data generated from masspeck gc x gc Chromatof .
I need help from the user about their experience. Thank you.
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