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- Posts: 74
- Joined: Wed Mar 25, 2020 8:52 am
Hello,
I run a large nr om MRM with narrow acquisition windows and it is a pain to update start and stop times for each window. The usually all change in same direction so I move all +- 0.05 min from time to time. There is no easy function that allow me to shift the entire MRM list in the masslynx software. Adjusting each MRM one at the time is very unpractical when there are 200 mrm that cant overlap.
I would like to have a table with all MRM settings and RT windows that can be modified in R or Excel as i see fit then pasted into the Masslynx experiment file. The .exp file is just a basic text file but they have not organised it as clean variables and a table so modifying this large file of text is not that easy. I does seems like it would be possible with some scripting work so I was wondering if anyone have found a ready solution for this?
from exp file into excel in this format
Function as the row with settings as columns.
Settings RT-start RT-end MS1 MS2 ConeEnergy ColissionEnergy
Function1 2.1 2.4 730 184 50 30
Function2 2.5 2.7 800 200 40 30
Then export back modified values into the .exp file?
I could then manage all experiments in table formats and manage them in SAS or R software.
I cannot be the only one looking for this solution. I am thinking a free software (maybe skyline) or a skript in R/Python/SAS.
Update: I have been able to import MRM data from excel and create masslynx experiment files frim the lists. Both Skyline and Waters Quanpedia worked for this.
In Waters Quanpedia I can set the RT but all MRM windows will have the same width as the one used in the template file. I wish to use different width of the MRM window for different compounds.
In skyline I can set the scheduled MRM window as I wish but it does not transfer correct to the .exp file for masslynx?
Anyone figured out to export a scheduled MRM method for masslynx from skyline where the start and stop times are registered correct in the exp file?
So close but not quite there to control all MRM data needed for the exp file in the excel file.
Regards,
I run a large nr om MRM with narrow acquisition windows and it is a pain to update start and stop times for each window. The usually all change in same direction so I move all +- 0.05 min from time to time. There is no easy function that allow me to shift the entire MRM list in the masslynx software. Adjusting each MRM one at the time is very unpractical when there are 200 mrm that cant overlap.
I would like to have a table with all MRM settings and RT windows that can be modified in R or Excel as i see fit then pasted into the Masslynx experiment file. The .exp file is just a basic text file but they have not organised it as clean variables and a table so modifying this large file of text is not that easy. I does seems like it would be possible with some scripting work so I was wondering if anyone have found a ready solution for this?
from exp file into excel in this format
Function as the row with settings as columns.
Settings RT-start RT-end MS1 MS2 ConeEnergy ColissionEnergy
Function1 2.1 2.4 730 184 50 30
Function2 2.5 2.7 800 200 40 30
Then export back modified values into the .exp file?
I could then manage all experiments in table formats and manage them in SAS or R software.
I cannot be the only one looking for this solution. I am thinking a free software (maybe skyline) or a skript in R/Python/SAS.
Update: I have been able to import MRM data from excel and create masslynx experiment files frim the lists. Both Skyline and Waters Quanpedia worked for this.
In Waters Quanpedia I can set the RT but all MRM windows will have the same width as the one used in the template file. I wish to use different width of the MRM window for different compounds.
In skyline I can set the scheduled MRM window as I wish but it does not transfer correct to the .exp file for masslynx?
Anyone figured out to export a scheduled MRM method for masslynx from skyline where the start and stop times are registered correct in the exp file?
So close but not quite there to control all MRM data needed for the exp file in the excel file.
Regards,
