Input files

Three input files (formally named taskTable, tgTable and quantTable) are used by the set of scripts :

Script \ Input	taskTable	tgTable	quantTable
analysis.R	X	X
checkRep.R	X		X
quantify.R	X		X

taskTable

This file defines the list of MS-DMS pairs to be analyzed.

It is a “comma” (,) delimited ‘.csv’ file. It can be edited using excel or Rstudio (safer).

Structure

MS_file	DMS_file	t0	CV0	dilu	Path
C0_AS_DV-1800_1.d.ascii	Fichier_Dims 20190517-000000.txt	0.08	6	0	Esquire_MSMS_Data/2019_A_Voir/20190517_AA/

Where:

• MS_file is an ASCII file, extracted using DATAANALYSIS. So far, only the ESQUIRE data files extracted using the profile option can be handled. It is stored in data or a sub-folder of data defined by Path.

• DMS_file is the corresponding DMS file. It is expected to be in the data folder.

• t0 and CV0 are used to convert the ESQUIRE time t values into DMS CV values.

• dilu was initially meant to be the dilution factor of the standard metabolites when spiked into a plasma (see checkRep). When you perform another type of experiment, you can use
  dilu as an index to specify, for example, the flow-rate of the modifier, the day of the experiment, the set of samples…

• Path allows you to organize your data within the ../data/ folder. Note that the DMS_files must be in the ../data folder. In the present example, only the MS file is expected to be found in the following folder: ../data/Esquire_MSMS_Data/2019_A_Voir/20190517_AA/.

Notes

• lines starting with “#” are not processed and treated as comments lines

• the date extracted from DMS_file (here ‘20190517’)
  and the root of the MS_file name (here ‘C0_AS_DV-1800_1’) are combined to tag the output figures and tables (e.g., ‘20190517_ C0_AS_DV-1800_1.results’)

tgTable

This file contains the list of compounds to be analyzed in each MS/DMS data set.

It is a “commma” (,) delimited ‘.csv’ file. It can be edited using excel or Rstudio (safer).

Structure

Name	Comments	m/z_ref	CV_ref
# Gly-AA	C2H5NO2H	76	-10.7
Ala-AA	90.054955	90.1	-7.6

where:

• Name is the given name of a metabolite,

• Comments is presently not used

• m/z_ref is the expected (approximate) m/z value

• CV_ref is the expected CV value (it can be omitted)

Notes

• lines starting with “#” will be considered as comment lines. In the present example, Glycine will not be analyzed.

quantTable

This file contains the list of compounds and internal references used for quantification.

It is a “comma” (,) delimited ‘.csv’ file. It can be edited using excel or Rstudio (safer).

Structure

Name	IS	CAA_Plasma	CAA_ref	CIS_ref
# Gly-AA	Gly-13C2	11.75	1750	26.7
Ala-AA	Ala-13C2	16.15	1750	20

where

• Name is the name of the compound, as used in tgTable

• IS is the name of the internal spiking compound. It should also be present in tgTable

• CAA_Plasma ???

• CAA_ref ???

• CIS_ref ???