pmartRdata: pmartRdata

In pmartR/pmartRdata: Example Data for pmartR Package

pmartRdata

Description

The pmartRdata package contains example datasets compatible with the pmartR package. These datasets include unlabeled (LC-MS/MS) and isobaric labeled (TMT) peptide, protein, metabolites (GC-MS and NMR), lipids (both negative and positive LC-MS ionization modes), and RNAseq. Some of the datasets were generated as part of the same experiments, as described below.

Data types

Experiment 1 Data: Host response to virus using human cells. This experiment includes isobaric labeled peptide data (TMT), negative and positive ionization mode LC-MS lipidomics data, and RNAseq data. Sample names across the different data types from this experiment have been harmonized, to allow data integration. These data are a deidentified subset from an experiment that has not yet been published. Samples included in this subset consist of human cells infected with one of three virus strains.

Experiment 2 Data: Human tissue samples. This experiment includes unlabeled peptide data (LC-MS/MS), the associated protein data, and metabolomics data (GC-MS). Sample names across the different data types from this experiment have been harmonized, to allow data integration. Note that the These data are a deidentified subset from an experiment that has not yet been published. Samples included in this subset consist of tissue samples from humans exhibiting three primary phenotypes.

NMR Data: Tomato plant samples. These data are publicly available via Biais et al. (reference listed below). Samples in this experiment each come from one of four different time points.

Technical Replicates Peptide Data: Mouse plasma samples. These data are a subset of the data used in Webb-Robertson et al. (reference listed below) and include biological samples associated with one of two levels of a factor, a dilution level of mouse plasma to Shewanella Oneidensis MR-1, and a technical replicate (two technical replicates per biological sample).

Data formats

Each type of data is provided in two formats. The first format is an S3 object class used by the R package pmartR. Data available as S3 objects 'pepData', 'proData', 'metabData', 'lipidData', ‘nmrData’, and ‘seqData’ are created by as.pepData, as.proData, as.metabData, as.lipidData, as.nmrData, as.seqData, respectively. The second format corresponds to the individual components of the S3 object classes, e_data - biomolecule expression data, f_data – sample meta information, and e_meta – biomolecule expression meta data. See pmartR for more details.

References

Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM (2014), Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Molecular & Cellular Proteomics. doi: 10.1074/mcp.M113.030932.

Biais B, Benard C, Beauvoit B, Colombie S, Prodhomme D, Menard G, Bernillon S, Gehl B, Gautier H, Ballias P, et al. (2014), Remarkable reproducibility of enzyme activity profiles in tomato fruits grown under contrasting environments provides a roadmap for studies of fruit metabolism. Plant Physiol 164 (3), 1204-1221. doi: 10.1104/pp.113.231241.

See Also

as.lipidData

as.metabData

as.nmrData

as.pepData

as.proData

as.seqData

pmartR/pmartRdata documentation built on Jan. 13, 2023, 3:52 a.m.