Parameter settings for LTQ-XL May 22, 2012, 01:50:34 PM 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 ppmS/N threshold: 6Alignment: min frac: 1mzwid: 0.050Statisticsp-value: 0.05Annotation: ppm error: 10Adduct added: M+ search for: Isotopes + AdductsThese 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.Thanksprao Quote Selected
Re: Parameter settings for LTQ-XL Reply #1 – May 23, 2012, 05:04:51 PM Metabolomics with the LTQ ? It might be challenging ...How many scans do have per feature ? Is it centroid mode data? What type of chromatography and gradient are you using ? Quote Selected
Re: Parameter settings for LTQ-XL Reply #2 – May 24, 2012, 04:03:59 PM 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.Thank youPrao Quote Selected
Re: Parameter settings for LTQ-XL Reply #3 – May 24, 2012, 05:15:04 PM MS1 needs to be in centroid mode if you want to use centWave. MS/MS is ignored for profiling.How many scans do have per feature, i.e. how many scans per chromatographic peak do you typically see ?it should be in the order of >5 for a reliable feature detection. Quote Selected
Re: Parameter settings for LTQ-XL Reply #4 – May 25, 2012, 01:06:34 PM 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.Thank youPrao Quote Selected
Topic: Parameter settings for LTQ-XL