| Title: | Saghatelian et al. (2004) FAAH knockout LC/MS data |
|---|---|
| Description: | Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. |
| Authors: | Colin A. Smith <[email protected]> |
| Maintainer: | Steffen Neumann <[email protected]> |
| License: | LGPL |
| Version: | 1.52.0 |
| Built: | 2026-10-10 11:01:18 UTC |
| Source: | https://github.com/bioc/faahKO |
xcmsSet object containing quantitated LC/MS peaks from the
spinal cords of 6 wild-type and 6 FAAH knockout mice. The data is a
subset of the original data from 200-600 m/z and 2500-4500 seconds.
It was collected in positive ionization mode.
data(faahko)data(faahko)
The format is:
Formal class 'xcmsSet' [package "xcms"] with 8 slots ..@ peaks : num [1:4776, 1:11] 200 201 205 206 207 ... ..@ groups : logi[0 , 0 ] ..@ groupidx : list() ..@ sampnames: chr [1:12] "ko15" "ko16" "ko18" "ko19" ... ..@ sampclass: Factor w/ 2 levels "KO","WT": 1 1 1 1 1 1 2 2 2 2 ... ..@ rt :List of 2 .. ..$ raw :List of 12 .. ..$ corrected:List of 12 ..@ filepaths : chr [1:12] ... ..@ profinfo :List of 2 .. ..$ method: chr "bin" .. ..$ step : num 0.1
The corresponding raw NetCDF files are located in the cdf
subdirectory of this package.
http://dx.doi.org/10.1021/bi0480335
Saghatelian A, Trauger SA, Want EJ, Hawkins EG, Siuzdak G, Cravatt BF. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry. 2004 Nov 16;43(45):14332-9.
## The directory with the NetCDF LC/MS files cdfpath <- file.path(find.package("faahKO"), "cdf") cdfpath list.files(cdfpath, recursive = TRUE) if (require(xcms)) { ## xcmsSet Summary show(faahko) ## Access raw data file ko15 <- xcmsRaw(filepaths(faahko)[1], profmethod = "bin", profstep = 0.1) ko15 }## The directory with the NetCDF LC/MS files cdfpath <- file.path(find.package("faahKO"), "cdf") cdfpath list.files(cdfpath, recursive = TRUE) if (require(xcms)) { ## xcmsSet Summary show(faahko) ## Access raw data file ko15 <- xcmsRaw(filepaths(faahko)[1], profmethod = "bin", profstep = 0.1) ko15 }
XCMSnExp object containing quantitated LC/MS peaks from the
spinal cords of 6 wild-type and 6 FAAH knockout mice. The data is a
subset of the original data from 200-600 m/z and 2500-4500 seconds.
It was collected in positive ionization mode.
data(faahko3)data(faahko3)
The format is:
MSn experiment data ("XCMSnExp")
Object size in memory: 4.59 Mb
- - - Spectra data - - -
MS level(s): 1
Number of spectra: 15336
MSn retention times: 41:32 - 75:14 minutes
- - - Processing information - - -
Data loaded [Tue Mar 24 13:28:38 2020]
MSnbase version: 2.13.2
- - - Meta data - - -
phenoData
rowNames: 1 2 ... 12 (12 total)
varLabels: sample_name sample_group
varMetadata: labelDescription
Loaded from:
[1] ko15.CDF... [12] wt22.CDF
Use 'fileNames(.)' to see all files.
protocolData: none
featureData
featureNames: F01.S0001 F01.S0002 ... F12.S1278 (15336 total)
fvarLabels: fileIdx spIdx ... spectrum (33 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
method: centWave
5627 peaks identified in 12 samples.
On average 469 chromatographic peaks per sample.
Alignment/retention time adjustment:
method: peak groups
Correspondence:
method: chromatographic peak density
206 features identified.
Median mz range of features: 0.10001
Median rt range of features: 28.965
325 filled peaks (on average 27.08333 per sample).
The corresponding raw NetCDF files are located in the cdf
subdirectory of this package.
http://dx.doi.org/10.1021/bi0480335
Saghatelian A, Trauger SA, Want EJ, Hawkins EG, Siuzdak G, Cravatt BF. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry. 2004 Nov 16;43(45):14332-9.
## The directory with the NetCDF LC/MS files cdfpath <- file.path(find.package("faahKO"), "cdf") cdfpath list.files(cdfpath, recursive = TRUE) data(faahko3) ## XCMSnExp Summary show(faahko3)## The directory with the NetCDF LC/MS files cdfpath <- file.path(find.package("faahKO"), "cdf") cdfpath list.files(cdfpath, recursive = TRUE) data(faahko3) ## XCMSnExp Summary show(faahko3)