___ XCMS analysis summary using Workflow4Metabolomics ___
Samples used:
| sample | filename | md5sum* |
|---|
| ko15 | ko15.CDF | 4698c36c0b3af007faf70975c04ccf2a |
| ko16 | ko16.CDF | afaeed94ced3140bc042d5ab6aeb16c1 |
| wt15 | wt15.CDF | d58a27fad7c04ddddb0359ddc2b7ba68 |
| wt16 | wt16.CDF | 29654e9f8ad48c1fbe2a41b9ba578f6e |
*The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.
Function launched:
| timestamp*** | function | argument | value |
|---|
| Wed Feb 7 11:15:25 2018 | Peak detection |
Object of class: CentWaveParam
Parameters:
ppm: 25
peakwidth: 20, 50
snthresh: 10
prefilter: 3, 100
mzCenterFun: wMean
integrate: 1
mzdiff: -0.001
fitgauss: FALSE
noise: 0
verboseColumns: FALSE
roiList length: 0
firstBaselineCheck TRUE
roiScales length: 0
|
| Mon Feb 12 15:31:11 2018 | Peak grouping |
Object of class: PeakDensityParam
Parameters:
sampleGroups: character of length 4
bw: 30
minFraction: 0.8
minSamples: 1
binSize: 0.25
maxFeatures: 50
|
| Mon Feb 12 15:31:19 2018 | Retention time correction |
Object of class: PeakGroupsParam
Parameters:
minFraction: 0.85
extraPeaks: 1
smooth: loess
span: 0.2
family: gaussian
number of peak groups: 125
|
| Mon Feb 12 15:31:27 2018 | Peak grouping |
Object of class: PeakDensityParam
Parameters:
sampleGroups: character of length 4
bw: 20
minFraction: 0.4
minSamples: 1
binSize: 0.25
maxFeatures: 50
|
| Wed Feb 14 09:55:13 2018 | Missing peak filling |
Object of class: FillChromPeaksParam
Parameters:
expandMz: 0
expandRt: 0
ppm: 0
|
***timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
Informations about the XCMSnExp object:
MSn experiment data ("XCMSnExp")
Object size in memory: 1.41 Mb
- - - Spectra data - - -
MS level(s): 1
Number of spectra: 5112
MSn retention times: 41:33 - 75:0 minutes
- - - Processing information - - -
Concatenated [Thu Feb 8 15:36:09 2018]
MSnbase version: 2.4.2
- - - Meta data - - -
phenoData
rowNames: ./ko15.CDF ./ko16.CDF ./wt15.CDF ./wt16.CDF
varLabels: sample_name sample_group
varMetadata: labelDescription
Loaded from:
[1] ko15.CDF... [4] wt16.CDF
Use 'fileNames(.)' to see all files.
protocolData: none
featureData
featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
fvarLabels: fileIdx spIdx ... spectrum (27 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
method: centWave
15230 peaks identified in 4 samples.
On average 3808 chromatographic peaks per sample.
Alignment/retention time adjustment:
method: peak groups
Correspondence:
method: chromatographic peak density
6332 features identified.
Median mz range of features: 0
Median rt range of features: 0
5979 filled peaks (on average 1494.75 per sample).
Informations about the xcmsSet object:
An "xcmsSet" object with 4 samples
Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)
Mass range: 200.1-600 m/z
Peaks: 15230 (about 3808 per sample)
Peak Groups: 6332
Sample classes: KO, WT
Feature detection:
o Peak picking performed on MS1.
o Scan range limited to 1 - 1278
Profile settings: method = bin
step = 0.1
Memory usage: 3.11 MB
Citations:
- To cite the XCMS package in publications use:
- Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)
- Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)
- H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)
- To cite the CAMERA package in publications use:
- Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)
- To cite the Workflow4Metabolimics (W4M) project in publications use:
- Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813