I can’t say what is best because that depends on what sort of data you have, but we have used SpectralWorks’ AnalyzerPro for GC/MS chemometrics. It is good for LC/MS data as well. Here is their website:

https://www.spectralworks.com/analyzerpro.html

My own MassMountaineer software has extensive chemometric tools for analyzing mass spec data, although it could work with any data in the form of x,y pairs: Here is the website:

massmountaineer.com

Of course, you can do almost any kind of chemometric analysis with R if you are comfortable in using its programming environment.

Dear Bhupendra Shrestha , When you mention three API peaks, are you referring to 3 chromatographic unresolved (partially overlapping) peaks? If yes, it seems you are trying to circumvent an analytical problem by using numerical tools instead of solving the problem itself (by optimizing your analytical method/procedure). I can tell you that you are, most probably enlarging your problem as you will need, when submitting a MA or a Variation to a MA, to properly justify and validate the use of “numerical/chemometric” methods in the quality part of the regulatory documentation. At that stage you will, most certainly, be asked to redo all the product development using properly validated procedures!

If you are working in a very early phase of the drug product development (with no GMP compliance) and with a tight budget I would recommend trying R or Python as they’re free to use – but again you will not most probably (I’m just guessing) be solving your problem.

Unscrambler X as well as OriginPro are commercially available and quite powerful - but not cheap.

Hope it helps, Regards, Luis