My lab operates an AB Sciex Q4000 with Analyst 1.5 software. We would like to develop methods to automate the integration of MRM peaks and be able to ship data to collaborators that does not require them to have Analyst software to do data integration and inspection.
Originally I was thinking that conversion to a netCDF is commonplace for many MS programs, but it seems less straight forward for Analyst? I am not married to the cdf format, just a format that could be subsequently imported into Matlab or easily integrated in other freeware programs.
After a little digging several options seem possible and two of them are part of the ProteoWizard project, therefore I was seeking advice about the best way to go forward.
1) ProteoWizard offers an "msconvert" option?
2) ProteoWizard offers "Skyline" option? - possibly MRM transitions can be extracted from wiff files - though I am not sure how this would work.
3) Apart from ProteoWizard I found reference to a wiff2dta converter. Presumably I could convert the dta to another format subsequently, however my search also suggested that dta files are significantly reduced in information and much of the data is lost in translation. I am not sure if this is an issue.
Apparently one challenge is that some software options require the conversion of each MRM one at a time which is not very practical in our case because we quantify isotopically labeled materials with many transitions.
I have limited expertise with the ProteoWizard suite which appears very extensive and comprehensive at first blush. I would like to avoid spending the the next several weeks trying to figure out which if any of the programs might work, therefore I am seeking your guidance. I suspect that as Analyst is a popular software - this is probably a frequent question and has a "best" approach - as deemed by the experts at ProteoWizard?
Can you please advise, thank you
Doug K. Allen, Ph.D.
USDA-ARS Research Computational Biologist
Donald Danforth Plant Science Center
975 N. Warson Rd.
St Louis MO 63132
Ph (office): 314- 587-1460