sneumann
commented
8 years ago Dear Jiaq, can I ask you to post this question to http://www.metabolomics-forum.com/ and send me the link of the post ? I know the answer, and then I can post it there. Yours, Steffen
Dear Gunnar,
I'm sorry to bother you again. Recently, I have met some unexpected problems handling metanolomics data by IPO. Here are the details.
(1) Instrument: UFLC-IT-TOF-MS (SHIMADZU) File type from vendor software (LCMSSolution, SHIMADZU): .lcd
(2) If I converted the .lcd files to .netCDF files by vendor software, (since the mass spectrometry switch between positive and negative models) the data were sorted by the scan time with one positive record followed by one negative record. IPO failed to pick peaks with the method “centWave”.
Then I tried to converte the .lcd files to .mzXML (or .mzData) files, and each .lcd file would generate two .mzXML files containing positive and negative records respectively. When handing the positive or negative data, IPO failed to detect isotope ions neither. I checked the .mzXML files by OpenChrom and found something strange. It seems that the mass data were un-centroided or false centroided. Part of the data at the same scan time sorted by mz values were below. m/z abundance 230.21 0 230.225 8832 230.239 15360 230.254 13184 230.268 0 256.232 0 256.247 15360 256.262 19712 256.277 13184 256.293 0
It is very different with the .netCDF file. m/z abundance 230.24 124278 231.24 8832 256.26 37504
The vender software seemed to be wrong when converting the .lcd files to mzXML files (or mzData).
How could I get the appropriate .netCDF files for IPO? I do really need a method to transform the .netCDF file to two separated .netCDF files with one containing the positive data and another containing the negative data. I have tried the R package “ncdf” to transform the files, but failed since I am not familiar with R.
Since the network of xcms-websites doesn’t work, I am sorry to interrupt you. Looking forward to your help and advises! Thanks in advance.
Best Regards, Jiaq Chen