Hello,
I am looking for free/open source software that can process files from SRM experiments (converted to an open format) and provide parameters such as peak start/end at x% height, fwhm, noise etc. Does anyone have any suggestions?
Many thanks
Hi,
I am not familiar with SRM experiment but what about MProphet? Here the link MProphet.org (http://www.mprophet.org/#Overview) and here the paper associated nature (https://www.nature.com/articles/nmeth.1584) or researchgate (https://www.researchgate.net/publication/50596725_MProphet_Automated_data_processing_and_statistical_validation_for_large-scale_SRM_experiments)
Elena
Hi VSO,
I've used skyline (https://skyline.ms/project/home/software/Skyline/begin.view) a fair bit in the past for metabolomics SRM data analysis. You can export peak areas, retention times (apex, start of integration, end of integration) and FWHM fairly easily (using document grid). I don't know if it generates a metric for noise (or S/N)...
The hardest part when getting started, is that you have to manually specify what transitions you want to look at (edit->Insert->Transition list). Skyline won't read the transition list from a file automatically.
Cheers,
Corey
I'm also not familiar with SRM/MRM data. But we have implemented a readSRMData function in MSnbase to read chromatographic data from mzML files. Would be nice to know if that works for you and what is missing. Note also that xcms can do now peak detection also on purely chromatographic data (i.e. Chromatogram/Chromatograms classes which are returned by the readSRMData function).