mtbls297: Comparative LC/MS-based profiling of silver nitrate-treated...

In sneumann/mtbls297: MetaboLights MTBLS297: Multiomics of tomato glandular trichomes reveals distinct features of central carbon metabolism supporting high productivity of specialized metabolites. Balcke et al. (2017)

Description

xcmsSet object from the data in the paper on "Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites." It was collected in positive ionization mode.

Usage

data(mtbls297)

Format

The format is:

Formal class 'xcmsSet' [package "xcms"] with 12 slots
  ..@ peaks           : num [1:83861, 1:23] 361 369 447 277 372 ...
...

Details

The corresponding raw mzML files are located in the mzML subdirectory of this package.

They were converted/reduced from the original MTBLS297 files with msconvert –32 -z –filter "scanTime [500,700]" –filter "threshhold absolute more 43" –filter "mzWindow [100,500]"

Source

http://www.ebi.ac.uk/metabolights/MTBLS297 https://github.com/sneumann/mtbls297

References

Gerd U. Balcke, Stefan Bennewitz, Nick Bergau, Benedikt Athmer, Anja Henning, Petra Majovsky, José M. Jiménez-Gómez, Wolfgang Hoehenwarter, Alain Tissier. Multi-Omics of Tomato Glandular Trichomes Reveals Distinct Features of Central Carbon Metabolism Supporting High Productivity of Specialized Metabolites. The Plant Cell (2017) DOI: 10.1105/tpc.17.00060

See Also

XCMSnExp

Examples

data(mtbls297)

## The directory with the mzML LC/MS files
filepath <- file.path(find.package("mtbls297"), "mzML")
filepath
list.files(filepath, recursive = TRUE)

sneumann/mtbls297 documentation built on July 14, 2020, 12:43 a.m.