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1
XCMS Online / Re: Issue with .cdf files
Last post by Jan Stanstrup -
You are looking at tic in masslynx but BPI in mzMine.
The spectrum looks weird. Like it is the wrong spectrum. I think the scan numbers could be offset. I suggest doing EIC of for example 195 so you are sure which scans actually correspond.
2
XCMS Online / Re: Issue with .cdf files
Last post by THBCCCU -
Hi so I have followed all of your instructions but i think maybe i have an issue with the scan event function, my spectrum in Mzmine matches my 2nd TIC in Masslynx but the 1st is completely different, could someone explain what is going on here?

(blue = Mzmine, Helpfully the top green = 2nd TIC in masslynx and red = 1st TIC in Masslynx and the spectrum is the other way around in colour)
3
Other / Workflow4Experimenters 2018 Course: Analyze your metabolomics data with Galaxy!
Last post by Etienne Thevenot -


During this "Bring Your Own Data" one-week course (8-12 october 2018, Paris, France), you will use Galaxy and the Workflow4Metabolomics online platform (W4M) to analyze your own LC-MS, GC-MS, or NMR data set. Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring on your data. 

Invited speakers: Christoph Steinbeck (Friedrich Schiller University - Jena) and Julien Boccard (University of Geneva)

Organization: Infrastructures for bioinformatics (ELIXIR-FR, IFB) and metabolomics (MetaboHUB).

Registrations (up to June 1st): http://workflow4metabolomics.org/W4E2018

Contact: contact@workflow4metabolomics.org

See you soon in Paris!
4
METLIN / Re: The METLIN database can not be accessed
Last post by siuzdak -
METLIN is running fine however certain regions have been attacking the site so we have had to restrict access to those places until the attacks stop.
5
METLIN / Re: The METLIN database can not be accessed
Last post by sally9135 -
yes, so do I
6
XCMS Online / Re: Processing IMS data on a short gradient with XCMS
Last post by ML -
Great! I will try that many thanks for your help!
7
CAMERA / Re: Feature Warning and Hanging at graph cross linking
Last post by Jan Stanstrup -
You have 106,874 features. That is an insane number. About 10 times what I think is reasonable to get. CAMERA chokes trying to build a network between all these features. With 800 pseudo spectra after the first CAMERA step you have an average of ~ 1000 features in each group. Some group might be much larger.
You should focus on understanding why you get so many features. It looks like peak picking issues since each sample have a very high number of peaks. Check the sanity of your settings. On the top of my head these are the things that could lead to that:
1) too low ppm (split peaks)
2) too low allowed minimum peak width (spikes could get picked)
3) too low allowed maximum peak width (split peaks)
4) No prefilter or too liberal settings (picking noise)
5) noisy data in general
6) contaminants with persistent presence together with liberal settings
7) Continuum mode data instead of profile mode data (important!)
8
CAMERA / Re: Feature Warning and Hanging at graph cross linking
Last post by hholm -
Hi Jan,

Thank you so much for the response. Yes very large data set. Here is the peakfilled XCMSnExp object before I turn it into a xset.
Code: [Select]
> x_filled
MSn experiment data ("XCMSnExp")
Object size in memory: 109.46 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 500238 
 MSn retention times: -1:39 - 30:21 minutes
- - - Processing information - - -
Data loaded [Fri Mar 30 17:59:13 2018] 
Filter: select MS level(s) 1 [Fri Mar 30 17:59:18 2018] 
 MSnbase version: 2.4.2 
- - - Meta data  - - -
phenoData
  rowNames: AE1319_A001_QE001613.mzXML AE1319_A002_QE001672.mzXML ... NetTrapQC107_QE002304.mzXML (623
    total)
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  [1] AE1319_A001_QE001613.mzXML...  [623] NetTrapQC107_QE002304.mzXML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F001.S0001 F001.S0005 ... F623.S3285 (500238 total)
  fvarLabels: fileIdx spIdx ... spectrum (28 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 28322726 peaks identified in 623 samples.
 On average 45462 chromatographic peaks per sample.
Alignment/retention time adjustment:
 method: peak groups 
Correspondence:
 method: chromatographic peak density 
 106874 features identified.
 Median mz range of features: 0.0052374
 Median rt range of features: 15.996
 19590141 filled peaks (on average 31444.85 per sample).

Is there a way for me to run CAMERA in parallel for step other than the peak annotation? I understand it makes a snow cluster for that but it doesn't seem there are built in ways to run the isotope finding, groupCORR, ect in parallel.

Are there other steps I should take to manage the size of the xset?
9
CAMERA / Re: Feature Warning and Hanging at graph cross linking
Last post by Jan Stanstrup -
"Found isotopes: 34751" indicates that you have an insane number of peaks. How many peaks in your xset? That is probably why it is hanging.
10
XCMS Online / Re: Processing IMS data on a short gradient with XCMS
Last post by Jan Stanstrup -
XCMS needs centroided data. If this is Waters data you can centroid your data in masslynx and then convert. See here: http://www.metabolomics-forum.com/index.php?topic=1247.msg3673#msg3673