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Topics - katy

1
Mass spectrometers / LC-MS pre-treatment and filtering
Hi everyone,
I have no experience with LC-MS data acquisition or analysis, but I should work on untargeted metabolomic datasets acquired by someone else previously.
Every plasma sample was analysed in triplicate. Therefore, when I open the entire chromatogram to do a primary visual inspection, the replicates of the same samples do not perfectly coincide. To say more, some peaks of the same sample seem to have a completely different profile in consecutive runs. In this case, should I consider one of the runs as an outlier and eliminate it?
Generally speaking, how should I pretreat the raw LC-MS data?
Another doubt is about the blanks. I noticed that all the samples were acquired without blanks; if I do not have blanks, how can I filter and normalise after my spectra?
I hope to be clear enough.
Thanks in advance!
2
Galaxy / Galaxy metabolomics workflow
 Hi everyone, I am new to the forum and metabolomics analysis. I am going straight to the point because I'm pretty desperate and hope someone can help me. :'( Please!
I am working with an untargeted UHPLC-MS dataset (plasma samples). After much research, I converted the data from Bruker to netCDF format for xcms analysis in R and Galaxy.
I have considerable doubts:
First, I have more spectra in positive than negative ionization mode. Moreover, the files of negative mode take up more memory and could not be loaded entirely to Galaxy (I tried different compression apps to reduce its dimension). Therefore, I split it into distinct and smaller datasets based on the categories. Finally, every smaller dataset is pre-processed separately(maintaining the same parameter of the treatments for all subsets). Is this considered a correct approach?
Once I obtained the data matrix with extracted ions for positive and negative ions, should they have the same dimension to be processed with a ''Camera.combinexsAnnox''(This function check annotation of ion species with the help of a sample from opposite ion mode.)
Any suggestions?