Development of bioinformatics tools/software related to P2M2 platform (IGEPP's Metabolic Profiling and Metabolomic Platform) activities. All the tools developed are accessible via the Galaxy instance of the Genouest platform (https://galaxy.genouest.org/)
Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs. A P2M2 workflow was built to obtain carbon isotopologue distribution of specific metabolites (complete list of metabolites available in the file "Metabolite.dat") from GC-MS raw data files. The input files for this workflow can be any GC-MS raw dataset that contains a column "Name" filled with each carbon isotopologue of each fragment considered and a column "Area" filled with the area of the integrated peak. The name of each fragment must be written exactly as specified in the "Metabolite.dat" file to ensure accurate correction with IsoCor. Example: the name "ProlineC2C5_TMS_m0" is for the GC-MS fragment m/z 142 (integrated peak) containing the C2-C3-C4-C5 carbon skeleton of proline and 1 TMS derivative. m0 refers to the carbon isotopologue monitored (m0 for m/z = 142, m1 for m/z = 143, m2 for m/z = 144, m3 for m/z = 145, m4 for m/z = 146). (2021-10-17) (2021-10-17) https://doi.org/10.15454/1I9PET
| Manufacturer | Model |
|---|---|
| GCMS Shimadzu | GCTQD (TQ8040) |
Get multiple "Internal Standard Report" from the OpenLabCDS software where are describe a list of compound in format row (columns : RetTime Type ISTD Area Amt/Area Amount Grp Name) The converter creates a summary that contains a header (a list of compounds) and a list of "Sample name" with associated values for a target column (RetTime,Type,ISTD,Area,Amt/Area,Amount,Grp,Name)
| Manufacturer | Model |
|---|---|
| Agilent | GC-FID Agilent 6890N |
Build Isocor input file from MassLynx report ("Quantify Compound Summary Report")
| Manufacturer | Model |
|---|---|
| Waters Acquity | HPLC TQD |