results/screeningfolder of your enviMass project. In the following, this is outlined for target screening results. The same applies to ISTD screening results by adapting the R object file names accordingly (shown partly in brackets below).
("res_IS_neg_screen") for the positive and negative ionization modes, repectively. Note that
project_foldermust state a valid path to your enviMass project folder, containing a
logfile.empfile. In summary, these three below outlined list levels are:
res_target_pos_screen[[X]]: screening results over X compounds and different adducts.
res_target_pos_screen[[X]][[Y]]: screening results over Y files for one compound and one of its adducts.
res_target_pos_screen[[X]][[Y]][[Z]]: different screening results for Z different peak combinations for one file and for one compound and one of its adducts.
where each name consists of a
ID_adduct_Remark_tag1_tag2concatenation. All concatenation entries expect for
adductrefer to columns in the → target compound table (ISTD) stored as
targets (IS)in the
dataframesfolder of your project, which can be loaded via
load(...)as well. Thus, each first-level list entry contains all the screening results for one compound and one of its adducts. This entry can (a) be empty if no screening matches where found for any of the used files or (b) contains itself another list of the length of the used files if at least one screening match was found for any of these files. For example,
gives you the IDs of files with screening matches for the first first-level entry in the list for compound with ID=201 and its M+H adduct. Again, file names are not given if no screening
matches where aqcuired (= empty entry in the second-level list) or yet a third-level list with valid peak combinations for different screening matches. For example,
lists all screening peak combinations for this first compound and the first screened file with file ID=5. In turn, file information such as file IDs or file names can be retrieved from
measurementsobject also located in the
dataframesfolder of your project (can be loaded but must NOT be manipulated). This third and last list level can be accessed via, e.g.,
and contains yet another list itself. Only one such list may be available if only one peak combination has lead to a screening result. Each such list contains another 10 entries, namely:
which each detail:
res_target_pos_screen[][][]$Peaks:The IDs of the indivual peak combination to match the theoretical centroided isotopologue pattern of the compound and its adduct.
$score_1:Matching score for peaks to be expected above the effective and rather conservative LOD.
$score_2:Additional matching score for peaks found below the effective LOD (optional).
$ppm deviation:Mass deviation of peaks from theoretical centroided isotopologue pattern.
$RT deviation from mean:Peak RT deviation from RT mean of all screened $Peaks.
$m/z:Masses of the peaks.
$Intensity:Intensity of the peaks.