Hello all,
as I am quite often away from the lab facilities, I would like to know if there are any open-source/freeware that I could use to analyse my data (obtained from Xcalibur v.1.0.2, ThermoScientific, .RAW format) on my computer. I have had a look already, but it seems that most of the ones I found work with command lines and/or are for GC-MS.
As I use R for statistical analysis, I have some knowledge in command lines, but I am a lot more at ease with a graphic interface.
I would mainly use it for the qualitative and quantitative analysis of MS/MS spectra, but I would like to be able to also have a look at the UV/Vis absorbance spectra.
What do you use for this kind of application? What do you recommand? Have you tested some of them and if so, which one would you recommand?
It might be relevant to note that I use Wondows 7 or 8. I can also use Ubuntu if there is no other choice.
Thank you very much in advance.
Wishing you a pleasant day.
Hello Paul - why not use Maxquant (http://coxdocs.org/doku.php?id=maxquant:start) as it is freeware and is excellent at analysing .raw data.
You do not mention what sample you analyse - this would also be useful to know.
Good luck & kind regards,
Peter
Please use Proteowizard's MS Convert Tool for free: http://proteowizard.sourceforge.net/downloads.shtml and with the ThermoMS File reader format tab active. Using this you can convert the .raw to most software readable .mzXML or .mzML formats which then can be used for all kind of down stream analyses such as mzMINE (http://mzmine.github.io/), or say Mass++ (http://www.shimadzu.co.jp/aboutus/ms_r/archive/en/index.html) where both can read any common file formats and both from GC-MS and LC-MS. For all the above any Windows is fine. Hardly any metabolomics tool work on Linux these days and R (run on Windows) is very popular and easy ! : ) For UV/Vis absorbance spectra, then you might like to use mzMINE as priority. All tools I mentioned above are FREE, have excellent GRAPHIC USER interface and are press button to install, run and use regularly.
"OpenMS/ OpenChrome" though free bit tricky and messy with having to download a lot of add-ins or plugins to make things work in a step wise manner.
If you are a Linux fan, then MASSyPup64 from Dr. Robert Winkler (http://www.lababi.bioprocess.org/index.php/14-sample-data-articles/78-massypup) is what you may go to!
Further, all 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!!! : )
Let me know also, if the above were not the answers that you were looking for!
Hope the above would help a bit!
Thanks a lot, and regards
Biswa
Thank you very much for all your answers.
In the mean time, I had found the MS converter tool from Proteowizard mentionned by Biswapriya Biswavas Misra. It is extremely easy to use and very practical as it can convert the files under .mzXML format which can be read by nearly every software. I am please with it so far.
Regarding the analytical softwares, I have downloaded and installed OpenMS and OpenChrom. The first one doesn't feel userfriendly at all and you need to know a bit about it before being able to use it. The second one is a lot more user-friendly, but as said above, you need to add a few add-ons, plus I could not found the way to specificaly select one single ion/fragment chromatogram by itself.
I was just about to try mzMINE as I have heard quite good reviews about it.
Thank you for the link towards your article Biswapriya Biswavas Misra.
Best regards.
Paul
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