>>What also came in mind when I reviewed the data today was that even though the DIA data should contain MS2 spectra for 75 Da >>to 325 Da (window width is evenly distributed: 75-125, 125-175,...) MS-DIAL only displayed a range from 75 Da to about 140 Da.
Maybe, this is due to either (A) experimental file problem or (B) the converted file problem. What is your instrument used? SCIEX? SWATH-MS? or the others? If sciex, what is your raw data format type (wiff or wiff2)? Please let me know your experimental/analysis detail, and if possible, please send some example data to me. Thanks,
Hiroshi
Hello Hiroshi,
I have already send you some example data about 1-2 months ago. Could you tell me if you have received these or if you are even working on this problem?
I was using the library for LC-MS and also noticed those few entries for LC-MS.. However just a few days ago I tried to do Identification for some spiked samples with the provided GNPS-Library. Out of the samples which were measured with a DIA method I received about 100 identified metabolites from over thousand(s) of features. Even when I "lowered" the identification parameters the number of identified metabolites did not change. Also, if I remember correctly, not all of the spiked metabolites were identified. Maybe you do already have an idea of what could be the reason for this with those information. Nevertheless I can post my parameters as soon as possible to give you more details.
Best,
Leon
For the identification I used a tolerance of 0.1 Da each and a 50% score cut off. This should definitely give me more than my 92 identified features... What also came in mind when I reviewed the data today was that even though the DIA data should contain MS2 spectra for 75 Da to 325 Da (window width is evenly distributed: 75-125, 125-175,...) MS-DIAL only displayed a range from 75 Da to about 140 Da. I do not know why that is the case.. My experiment file is just as the one that is provided and I also did not set any m/z limitation in the settings.
It would be such a relief to know what the reasons for my failure with MS-DIAL are
I was using the library for LC-MS and also noticed those few entries for LC-MS.. However just a few days ago I tried to do Identification for some spiked samples with the provided GNPS-Library. Out of the samples which were measured with a DIA method I received about 100 identified metabolites from over thousand(s) of features. Even when I "lowered" the identification parameters the number of identified metabolites did not change. Also, if I remember correctly, not all of the spiked metabolites were identified. Maybe you do already have an idea of what could be the reason for this with those information. Nevertheless I can post my parameters as soon as possible to give you more details.
I tried to use the HMDB library (.msp, provided from mona) for identification with MS-Dial. No matter how low I am going with the identification parameters, MS-Dial displays 0 matched features. I already ran into a similar problem before where MS-Dial would not match any features when using the provided libraries (http://prime.psc.riken.jp/compms/msdial/main.html#MSP). So I switched from a German to an English OS which then worked fine. With the HMDB however neither German or English OS provide any matched features within MS-Dial.
So if anyone knows how to use the HMDB in MS-Dial for identification I would be glad to hear about it
My intention was just to get feedback about which software is mostly used from other people. With all programs I have tried minor issues occured so that is why I tried to get a glimpse of commonly used software. Just to give you some examples: XCMS - Identification works but the output contains multiple results with no clue how these are sorted or why there are empty names and there is no option to do quantification with the data. Also there is no way to export the identificated compounds to e. g. Skyline for quantification. MzMine - Matching of precursor to according MS2 spectra did not work so I could only do identification with precursor information. Results also did not conclude anything, just an empty .tsv.
I also tried several other programs but none really worked in a way that I can trust the identification results and either quantificate within that program or export e. g. an .msp file to skyline. As discussed in my other post I will try to use the HMDB from mona for identification in MS-Dial but I do not know whether I can quantificate the data within MS-Dial or if there is any other way for quantification.
Nevertheless I am still curious to hear what software is commonly used in the untargeted metabolomics community
I know that the risk of getting false annotations is very high but that is why i wanted MS-Finder to only respond with compounds that have at least a score of 6 which i set as my limit. The problem is that MS-Finder does not filter these results and therefore results with a score lower than 6 are getting displayed. Maybe i should give sirius a try again and also try out the HMDB from mona in MS-Dial instead of just only in Skyline... I am fearing that other libraries may not contain all metabolites that are included in the sample or that other compounds (that just can not be in the sample or do not make sense) in the libraries falsely match some signals. Is it also possible to do the quantification with MS-Dial?
I just posted my first topic where I am asking for suggestions about Software for untargeted metabolomics (http://www.metabolomics-forum.com/index.php?topic=1572.new#new). As described in that topic, I already tried several common used softwares like MS-Dial and MS-Finder. The problem for me with MS-Finder is that I do not really trust those results... The main reason is that often the scores of the structure finder results are very low even though I adjusted the minimal score value to be 6 in the parameter settings.
Are any of you using MS-Finder for identification purpose and could anyone help me with this problem?
I am currently working on Metabolomics for my bachelor thesis, so i am quite new to this topic. My latest problem is to find the right software for untargeted Metabolomics. I already tried several of the most common ones but nothing really seems to work for me. I am hoping that some of you could suggest Software that you are using. The tasks that have to be done are matching precursors to according MS2 spectra (which is called deconvolution i guess?), identification and quantification. I would also use multiple softwares to do this, but the import and export should be compatible. If there is no other way R could also be an option, but I do not have a lot of experience with R so I would be glad to not use R .
