4.4 Example data
The patRoonData and patRoonDataIMS packages contain HRMS and IMS-HRMS data, respectively, that can be used to explore the workflow. The data files are already exported in .mzML format and therefore ready to use. Furthermore, these packages also contain example suspect and internal standard lists, which will be explained in the next sections. The following functions can be used to obtain the example data:
# get analysis information for example data, which can be used directly for feature detection
patRoonData::exampleAnalysisInfo("positive")[, c("analysis", "replicate", "blank", "path_centroid")]#> analysis replicate blank path_centroid
#> 1 solvent-pos-1 solvent-pos solvent-pos /usr/local/lib/R/site-library/patRoonData/extdata/pos
#> 2 solvent-pos-2 solvent-pos solvent-pos /usr/local/lib/R/site-library/patRoonData/extdata/pos
#> 3 solvent-pos-3 solvent-pos solvent-pos /usr/local/lib/R/site-library/patRoonData/extdata/pos
#> 4 standard-pos-1 standard-pos solvent-pos /usr/local/lib/R/site-library/patRoonData/extdata/pos
#> 5 standard-pos-2 standard-pos solvent-pos /usr/local/lib/R/site-library/patRoonData/extdata/pos
#> 6 standard-pos-3 standard-pos solvent-pos /usr/local/lib/R/site-library/patRoonData/extdata/pos# negative ionization IMS data
patRoonDataIMS::exampleAnalysisInfo("negative")[, c("analysis", "replicate", "blank", "path_ims", "path_centroid")]#> analysis replicate blank path_ims path_centroid
#> 1 blank-neg-1 blank-neg blank-neg /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/ims /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/centroid
#> 2 blank-neg-2 blank-neg blank-neg /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/ims /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/centroid
#> 3 blank-neg-3 blank-neg blank-neg /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/ims /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/centroid
#> 4 standard-neg-1 standard-neg blank-neg /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/ims /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/centroid
#> 5 standard-neg-2 standard-neg blank-neg /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/ims /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/centroid
#> 6 standard-neg-3 standard-neg blank-neg /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/ims /usr/local/lib/R/site-library/patRoonDataIMS/extdata/negative/centroid#> name mz rt SMILES
#> 1 DEET 192.1383 355.8 CCN(CC)C(=O)c1cccc(c1)C
#> 2 Diglyme 135.1016 252.0 COCCOCCOC
#> 3 Dimethametryn 256.1590 372.6 CCNc1nc(nc(n1)SC)N[C@@H](C)C(C)C
#> 4 Irgarol 254.1434 370.8 CC(C)(C)Nc1nc(nc(n1)SC)NC2CC2
#> 5 Prometryne 242.1434 364.8 CC(C)NC1=NC(=NC(=N1)SC)NC(C)C#> name mz rt formula SMILES mobility_[M+H]+ InChI InChIKey neutralMass CCS_[M+H]+
#> 1 1H-benzotriazole-D4 124.0807 248.10 C6H1[2]H4N3 <NA> 0.544 <NA> <NA> 123.0735 120.542960528345
#> 2 Atenolol-D7 274.2143 199.34 C14H15[2]H7N2O3 <NA> 0.756;1.017 <NA> <NA> 273.2070 158.848376201002;213.6888870323
#> 3 Atrazine-D5 221.1324 335.87 C8H9[2]H5ClN5 <NA> 0.706;1.081 <NA> <NA> 220.1252 149.983743911608;229.649330266924
#> 4 Bezafibrate-D6 368.1530 358.16 C19[2]H6H14ClNO4 <NA> 0.857 <NA> <NA> 367.1457 177.928028244888
#> 5 Caffeine-13C3 198.0977 288.04 [13]C3C5H10N4O2 <NA> 0.655 <NA> <NA> 197.0904 140.055903653215