The protocol will depend on what you want to analyse. Follow the protocol and make precise standards. Any other analysis not required just to LC-MS prep. You can do any other analysis for additional results
First you perform TLC analysis. If Rf value is greater then go to Column chromatograpgy . if volatile/low b.p. samples are present go GC-MS. if samples are non-volatiI / solid then go to LCMS analysis.
You can do LC-MS but preliminary TLC is very important. Also, perform literature search to know the classes of compounds in your plant material to ease the interpretation of the LC-MS results.