It sounds like you're trying to re-create our MassHunter Mass Profiler software! This is exactly what it is designed to do:
Here's the quick start guide: https://www.agilent.com/cs/library/usermanuals/public/G3297-90017_MassProfiler_QuickStart.pdf
While the Mass Profiler looked to be what I was trying to do, I do not believe I have that software... I have the 2011 B.05.00 version and could not find a disc for the mass profiler. Is there a possibility I could do something similar with just the Quantitative Analysis software and the PCDL?
Hi tylerfunke, unfortunately Qual does not have a concept of a "Blank" data file. It cannot perform the required 'alignment' necessary to ensure that two features which share the same mass are the same compound - and therefore has no mechanism to remove a set of compounds from another set. If restricted entirely to Qual - I would do this by exporting the feature lists found in each data file - right-click on the compound list - and export to Excel. Then do my workup in excel to:
1.) Align the compound lists
2.) Find differences between them
There is separate tool called Profinder (which is free) which is capable of recursive 'find by molecular feature'. This will use a feature found in one data file to more thoroughly search for that feature in other data files (and supports chromatographic warping (to fix retention time shifting issues)). Profinder ships on the LCMS Supplemental Disk (version B.09, part number G3336-60108) which you can download from agilent.subscribenet.com. If you're having trouble accessing agilent.subscribenet.com - you can call our online technical support number (Contact Us | Agilent, option 3, then 2) and request free media replacement (or a download link for the same).
Profinder does not do fold change analysis. You would still need to do that part by hand - but the alignment should be taken care of for you. Profinder, like Qual, produces a compound list which can be exported to excel for you to do your own further analysis. This is basically the same workflow I described above for Qual - but Profinder is geared for cross-datafile feature finding. The real Agilent solution for this problem is to use Profinder to do the feature finding and alignment, then use Mass Profiler or Mass Profiler Professional to do the statistical and fold-change analysis.