are you doing a scanning of the compounds? have some standard?, what type of HPLC column has and which ones are your conditions of your method? regards
First you will have to do lot of referencing for the known compounds in your plant and try to find out methods for detecting the same..may be you could do simple tlc for identifying known compounds..
can you specify the compound name?. if it is volatile go by GCMS; low cost and fast. if the compound is non- volatile go by HPLC-DAD/VWD and if you have reference standard (pure compound with known purity) (or commercially available.
if the reference standard is not available go by LCMS;
First rule for LC-MS is ionization of the compounds.
If you could not do ionization, you can not go further anymore.
You can use some ionization reagets for this purpose as well.
Please do not confuse chromatography (HPLC) and spectroscopy (MS).
You can use LC (or HPLC) for chromatographic separation of compound from the mixture.
However, MS is necessary for spectroscopic information of the target compound.
For spectroscopic evaluation, only single compound information is valuable like your fingerprint.
If there are more then one fingerprints on it (mixed), you can not identify the compound by usig a single MS. You need at least MS-MS and/or another spectroscopic techniques for identification.
HPLC-MS is a hyphenated technique used for exact identification of pure or separated molecules through HPLC. LC-MS is a soft ionisation technique and after ionisation quasi ions forms. There are two major techniques of ionisation : ESI and APCI(positive and negative). After ionisation you will get Molecular wt+ H+, H-, NH4+ etc its depend upon you are using positive mode or negative mode. ESI mainly used for the polar compounds and soluble in water. API technique is used for non-polar compounds.