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Topics - prao

1
XCMS Online / Parameter settings for LTQ-XL
Hello,
  First of all congratulations on graduating from the beta version to the production version ! I was playing around with my metabolomics data acquired on an LTQ-XL (older Thermo machine) and started with the default settings on different instruments since there is no separate parameter for LTQ-XL. Used the same parameter settings as the single quad and also many of the orbitrap settings but none of my masses are detected (The program throws the error stating "no features Detected". During one such search search, the parameter settings for the UPLC/QTOF worked after tweaking a few parameters (by worked I mean it did not throw an error about no features detected). Encouraged by this I started exploring different options by changing to the UPLC/QTOF settings to-
Feature Detection:  50 ppm
S/N threshold: 6
Alignment:
min frac: 1
mzwid: 0.050
Statistics
p-value: 0.05
Annotation:
ppm error: 10
Adduct added: M+
search for: Isotopes + Adducts

These settings detect only some of the ions I can see manually but ignores many of them. I was wondering if you could possibly point me in the right direction as to what parameter settings might work for the LTQ-XL and whether you would be kind as to add a separate parameter in the instrument list.

Thanks
prao
2
Sample preparation / Filters for sample clean-up
Hello,
    I am kind of getting in to the metabolomics area from Proteomics and wanted to know if there are any suggestions as to sample cleanup after deproteinizing the serum with organic solvents. I have used C18 for peptides but using that for metabolites seems to be biased for hydrophobic ones. Are there any low binding filter materials that can be used. Also, I do not know if sample cleanup will help in enhancing the intensities of metabolites using 100% methanol for extraction. I am getting extremely weak signal intensities. Instrument is a Thermo LTQ. Any suggestions for cleanup would be highly apreciated.

Thank you