Since the MS1 in the current dataset is in Profile mode, can I use the parameters for Matched Filter settings. I am running another sample in centroid mode for MS1 data for my standards to be amenable for use with CentWave.
For the previous runs the scans per feature is around 10 or more. This is a very simple mixture of small molecules and all of them have good intensities and I can manually annotate them but I guess it is not being detected by the software because the parameters I am setting may be wrong. I would appreciate any help in this regard.
Thanks for the reply. We are currently running a top 6 method with a collision energy of 35. The MS is in profile mode and the MS/MS is in Centroid mode. We have a Thermo LC with a C18 column and nanospray. The ionization is ESI and fragmentation is CID. We are using a 2 hour gradient. The current material that I am injecting is a mixture of small molecules such as glucose, sucrose, leucine, tryptophan and not the actual experimental samples (serum) yet. I first wanted to test out with XCMS whether I can see a handful of small molecules whose masses I know before injecting the complex samples. The search IDs I had run if you want to take a look are 111543, 111423 and 111421.
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 Paul for the prompt reply. I tried these methods of extraction but my problem was that the column clogged in the nano-spray mode and I need to clean-up my sample using some kind of non-biased filter which will help filter out particulates produced during the preparation of the sample. Please let me know if you have any suggestions. I have used the centrifugal method but the column still clogs 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.
