FT IsoR MS data processing library
In order to measure the isotopic ratio of each elements (CHNO) in a given sample, you need to convert the .raw files to .mzML file using a converter software such as MSConvertGUI. In a routine experiemnt the isotopic ratio will be determined in MS/MS scans with HCD 50. To convert the file from .raw format one should add HCD and MS 2 as filters before converting the .raw to .mzML.
To have a nice information about the samples and experiment, you need to provide a .csv file (Experiment Design) with the name of these columns in the same order:
Mandatory fields:
File : Name of the file with .csv at the end
Sample : Name of the sample as you want to see in the result
Loading : Amount of sample loaded into LC-MS in ng (1000ng = 1ug)
Start : Starting time accoring to retention time, in min (0)
End : Ending time according to retention time, in min
gC : 13C/12C ratio, if it is available
gN : 15N/14N ratio, if it is available
gH : 2H/1H ratio, if it is available
gO : 18O/16O ratio, if it is available
Followed by experiment information - Note that the column header should be presented in the Experiment Design file but can be left out unfilled
Description : Information about the experiment
Aim : Goal of the experiment
Date : Date of experiment
Experimenter : Responsible person
Method : Method used in the analysis
No.Sample : Number of samples
Replicates : Number of replicate per each sample
Other : Any other information
Samples : Name of the samples
Controls : Name of the controls
No.Controls: Number of controls
LC.Gradient: Information about the LC separtion
Duration : Analysis duration time
Instrument: Specification on the used instruments
MS1 : Specific details about MS scans, e.g. scan range, number of microscans...
MS2 : Specific details about MS/MS scans, e.g. scan range, number of microscans...
Then, use the "ProcessExperiemntDesign_()" function where you need to provide the above .csv file as the file argument, and two list for amino acids of interest. The first list is for those amino acids that you want to analyze in your samples (ioi), and the second list is the amino acids that you want to see the graphs on them in the output result (ioi_).
Note that the list can be a list or matrix of string where each amino acid is shown with its designated one letter code.
For example : c("G","P","L\I") ---> Glycine, Proline and Leucine/Isoleucine are the amino acids that one is looking to analyze.
Link to PAIR-MS online version
Here you can see the infogram of how to use the online version.
