[W4M] XCMS analysis summary

sample	filename	md5sum^*
QC1_014	QC1_014.mzML	9e093906811d11c0b14de7a9c2171a75
QC1_008	QC1_008.mzML	b609cb66b0cd926a833d63cf5c529622
QC1_002	QC1_002.mzML	79b4ca15faab323ebd6608c5427b5448
HU_neg_192	HU_neg_192.mzML	5f60b7526c5dbf93972cfe1941739c2c
HU_neg_173	HU_neg_173.mzML	5a23e8996d4cb5d020c3399f9fad044e
HU_neg_157	HU_neg_157.mzML	e1e50308e9c440d885e8530302a1e2a2
HU_neg_123	HU_neg_123.mzML	77cff3c9ed4a9c00d05ec83308f69d6e
HU_neg_090	HU_neg_090.mzML	881d4e94b0de1f6aa7ae931e897348c8
HU_neg_048	HU_neg_048.mzML	cb133446f5137d0cf50ad9709f9c55f7
Blanc16	Blanc16.mzML	1f2ab054920c04ebed901942207509be
Blanc10	Blanc10.mzML	58e12f36b05e51671058b955c5c28d99
Blanc05	Blanc05.mzML	0a12e74200c736727c73fbb36429d22b

^*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
Wed Feb 15 11:08:55 2023	Peak detection	Object of class: CentWaveParam Parameters: ppm: 3 peakwidth: 5, 20 snthresh: 10 prefilter: 3, 5000 mzCenterFun: wMean integrate: 1 mzdiff: -0.001 fitgauss: FALSE noise: 1000 verboseColumns: FALSE roiList length: 0 firstBaselineCheck TRUE roiScales length: 0
Wed Feb 15 11:14:01 2023	Peak grouping	Object of class: PeakDensityParam Parameters: sampleGroups: character of length 12 bw: 5 minFraction: 0.9 minSamples: 1 binSize: 0.01 maxFeatures: 50
Wed Feb 15 11:31:52 2023	Retention time correction	Object of class: PeakGroupsParam Parameters: minFraction: 0.7 extraPeaks: 1 smooth: loess span: 0.2 family: gaussian subset: number of peak groups: 38
Wed Feb 15 11:37:08 2023	Peak grouping	Object of class: PeakDensityParam Parameters: sampleGroups: character of length 12 bw: 5 minFraction: 0.9 minSamples: 1 binSize: 0.01 maxFeatures: 50
Wed Feb 15 11:57:50 2023	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: 6.34 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: 0:0 - 19:0 minutes
- - - Processing information - - -
Concatenated [Wed Feb 15 11:12:56 2023] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: QC1_014.mzML QC1_008.mzML ... Blanc05.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] QC1_014.mzML...  [12] Blanc05.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S2022 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 223790 peaks identified in 12 samples.
 On average 18649 chromatographic peaks per sample.
Alignment/retention time adjustment:
 method: peak groups 
Correspondence:
 method: chromatographic peak density 
 5100 features identified.
 Median mz range of features: 0.004679
 Median rt range of features: 1.8432
 4792 filled peaks (on average 399.3333 per sample).

Informations about the xcmsSet object:

An "xcmsSet" object with 12 samples

Time range: 0.5-1139.6 seconds (0-19 minutes)
Mass range: 53.002-989.2216 m/z
Peaks: 223790 (about 18649 per sample)
Peak Groups: 5100 
Sample classes: QC, sample, blk 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2039 
Profile settings: method = bin
                  step = 0.1

Memory usage: 39.5 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

_ XCMS analysis summary using Workflow4Metabolomics _

Samples used:

Function launched:

Informations about the XCMSnExp object:

Informations about the xcmsSet object:

Citations:

___ XCMS analysis summary using Workflow4Metabolomics ___

Samples used:

Function launched:

Informations about the XCMSnExp object:

Informations about the xcmsSet object:

Citations:

_ XCMS analysis summary using Workflow4Metabolomics _