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Topic: CAMERA to Metabosearch? (Read 6820 times) previous topic - next topic

CAMERA to Metabosearch?

Greetings,
I have run into a problem trying to replicate another studies analysis.  The study is "LC?MS Based Serum Metabolomics for Identification of Hepatocellular Carcinoma Biomarkers in Egyptian Cohort" by Xiao et. al. 2012.  I initially tried contacting the lab, who were very polite, but the individual who did the analysis is gone.  Therefore I hope someone here can help.

The workflow for the study was xcms -> CAMERA -> features selection (two-way ANOVA) -> convert to neutral monoisotopic masses -> MetaboSearch

Now, I have acquired the mass spectrometry data and reanalyzed it as follows for the negative ionization runs:

neg <- Sys.glob(file.path("~/Downloads/ISAcreatorMetaboLights_1.7/isatab files/MTBLS19/All/", "*NEG.CDF"))
xsneg <- xcmsSet(neg)
xneg <- fillPeaks(group(xsneg))
xsaneg <- annotate(xneg)
write.csv(getPeaklist(xsaneg), file = "~/Desktop/HCC_negative.csv")

I afterwards split the data into the appropriate comparisons for me to implement an alternative feature selection method and subset the results.  Herein I reach my problem.

I am unable to upload the subset files into Metabosearch.  They subset files are .xlsx format, column names are correct, but I can't get them to upload.  I have discovered that if I omit some adducts, such as [M+H-CO2], then a shortened file will upload.  This leads me to my first question, is Metabosearch unable to accept certain adducts?

My second question, how would one convert the mz values to the neutral monoisotopic values from the camera output?  If I can convert them I would be able to avoid the aforementioned compatibility problem and just upload the mz values.  This may actually be something simple that I just can't see at this point but any guidance would be immensely appreciated.

Regards