Hello,
greetings!
I am recently working with MZmine 2 software for identification of plant metabolites. I have certain queries on setting the parameters to analyze my results. I tried using this software, but I think, I hardly know anything about it . I face troubles each time when I need to put parameters such as following:
1. m/z tolerance : How to decide m/z tolerance for steps like Chromatogram builder/ Peak Normalization/ Alignment and so on. I am using the same value as given in manual( 0.02 -5.0)
2. m/z or RT tolerance Weight:How to decide or what are the bases of deciding m/z weight or RT weight in"Alignment step"? How should I know what is this? "Help" option does not help me either. I used the same as in the manual. DO NOT know how correct I am doing.
3. Noise level or Baseline: Is Noise level or baseline same thing? Secondly, How to choose/ decide this? What I understood from "Help", it is the minimum height of the peak below which every other peak would not be counted. Keeping this in mind, I chose that peak from base peak chromatogram, which shows m/z labeling and is smallest among all the peaks which are labelled with m/z on them. Is this correct way to choose it?
Overall, Please help me understand how to decide the values to fill in parameter box under each step till PCA and log ratio step.
I know this is so much I am asking you, but believe me I a student a biology who never dealt with physics and software like this and on top of that Nobody in my dept. knows how to work with this software, not even my supervisor under whom I am working.
Thank you so much for your kind understanding and quick reply. Looking forward to your answer!
Best regards, Timsy
Hello,
The best way to tackle these problems would be to-
1. Consult/ ask your question at: http://www.metabolomics-forum.com/index.php?board=31.0 dedicated mzMine Q and A forum at the Metabolomics Society Forum.
2. mzMine developer discussion: http://mzmine-devel-developer-discussion.970458.n3.nabble.com/
3. See some videos like :https://www.youtube.com/watch?v=VS_Zpyl5chQ
4. Consult here: http://mzmine.github.io/support.html
Beyond all those basic steps, even to answer your questions, any one would need the following
1. Which instrument, chromatography system, MS detector- LC-MS, ToF, ESI, which LC systems UPLC etc.? etc. information are needed. All such details will help one determine the m/z tolerance for your data!
2. Also needed are instrument's mass resolution, resolving power, scan speed, entire chromatography run duration etc. as well. This will determine your m/z and RT (chromatography) tolerance weight etc
3. In metabolomics it is hard to determine and specify a baseline (aka- noise level!) for the entire duration of chromatography i.e0-20 or 0-40 minutes etc. whatever you have used. Your approach is manual. A better approach would be to see as to how many m/z peaks are listed when a certain intensity cut off is used. A typical signal/ noise ration of 5, 25, 50, 100 can be used and again, depends on your mass spec system in use! Typically peak 'area' (and some people choose peak 'height' for accuracy in certain applications) values are chosen as cut offs for signals to differentiate them from the noise!
Another quick way would be to ask Tomas Pluskal here https://www.researchgate.net/profile/Tomas_Pluskal , who created mzMINE and he would be happy to help as usual, I believe so.
Also not a good idea to do PCA or other statistical analysis using mzMINE. There are a lot of tools available to perform statistical analyses of the metabolomics data.
Majority of the freely available tools, software, and databases from 2014-2015 for your analyses have also been recently summarized/ reviewed by us at Updates in metabolomics tools and resources: 2014–2015 (http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/abstract), please check out the Table-1 and find your tools!!! Self promotions apart, there are a lot of statistical tools that can take care of statistical analysis once you are done with the data extraction (compound IDs (m/z, retention times) and peak areas or intensity counts under the peaks: )
Thanks,
Biswa
I never had physics as well though and was always a biologist. : )
Follow MS-DIAL in that case: https://www.nature.com/articles/nmeth.3393 and downloadable here: http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/ developed by the Fiehn lab which is SUPER FAST! : )
Timsy -- Do you know which information does MZmine use to search for metabolite ? Biswapriya Biswavas Misra
MZmine is not great for "annotation" and does not do so for MS/MS (does not facilitate spectral DB search). But it does so for accurate mass (MS1) searches based on KEGG, BioCyc, HMDB, ChemSpider among a few others whicha re in built and once can choose to search some of those.
Thanks,
Also, please, join the metabolomics Society’s Forum: http://www.metabolomics-forum.com/index.php?action=forum;?action=forum#c12 to ask more specific questions on each software when you have more detailed questions and doubts! For example: http://www.metabolomics-forum.com/index.php?board=31.0 and http://www.metabolomics-forum.com/index.php?board=98.0 on the two tools that we are discussing. Joining the forum is free and registration is fast!
Thanks,
Biswa
Hello,
right now I'm in the same situation( I'm a microbiologist )!
I can't find a user's guide that explains how to set the parameters according to the sample used !!
good luck for us
Timsy - a
Thank you!
I'm at the beginning of the adventure.
I can't find detailed guides ?
good luck for us -_-
Regards ,
Rima
Am getting "Failed to open the project: java.util.zip: ZipException:Zip End Header not found (Zipfile.java:1470" error. Any help pls!
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