I must sadly and repeatedly declare that HPLC-MS is not the quantitative method. Only HPLC-photometric (photometer and/or fluorometer) and refractometric (Refractive Index Detector; RID) methods give quantitative results.
Mass Spectrometry (MS) is depended on the gasification of each molecules in the specimens, and it detects extremely small area. Electron Microscopy (EM) is also not quantitative, since it detects extremely small area. I have kindly been informed from a kind and honest engineer of MS of Shimadzu Co., Kyoto, Japan, by the telephone that "MS is not a quantitative detector" (my unpublished experience at the University of Tokyo, Tokyo, Japan). I am now only praying that this kind engineer is safe in Schimadzu Co.
By the way, HPLC-photometric detection becomes to be quantitative when high-recovery analysis is achieved (please see files; SEC column 300 A silica for HPLC-Surfactant-SEC and Lysozyme by RP-HPLC for RP-HPLC).
If structural information is necessary, then MS, IR, or NMR should be used after the quantitation and the fractionation by HPLC-photometric method. It is important that fractionation should be carried out by considering the delay from the photometric detecter to the fractioning tube (tube volume should be measured) and the flow-rate of the eluent (my unpublished experience).
Furthermore, we have measured and determined biotin (vitamin H) and lipoic acid (thioctic acid) by HPLC-fluorometric-affinity method (please see files; Netherlands Biotin, Wide range of Biotin, and Lipoic acid Avidin).
HPLC with a photometric detector does NOT provide any structural information and would NOT be considered a means of identification of a metabolite or degradant. Additionally, many of the degradants and impurities present in drug products are well below the detection limit of UV or RI. There are an abundance of metabolite detection and quantification methods published; a simple Internet search on your part would turn up dozens of papers for you to read. FDA does not publish metabolite methods; you must do your own work to submit to FDA.
Dr. Hayakawa has repeatedly and incorrectly stated that MS is not a quantitative detector, despite the overwhelming evidence in the literature stacked against him. MS is not as precise as UV for compounds with a chromophore that are well separated from all other potential interferents, and the working range of MS is significantly lower than that of UV. However, it most certainly is a quantitative detector and has been used successful as such for decades. Additionally it provides qualitative information that UV or RI cannot.
I do not agree with Dr. Hayakawa. MS is definitely a quantitative technique along with it's ability to provide qualitative information. I am associated with Shimadzu instruments for a long time. We are using our Shimadzu MS system for quantitative analysis very frequently. All you require is reference standards for creating calibration curves. MS has wonderful applications in the field of metabolomics.
I completely agree with Mark Krause. I am using Bruker and shimadzu's LC-MS to quantify some pharmaceuticals in an environmental samples.....very low levels. The only thing you need is standard. For identification of metabolites, I would recommend any high resolution mass spectrometry such as the QTOF and Orbitrab. In our lab, we use Impact-II QTOF (Bruker) for identification of metabolites (Both targeted and untargeted). But if you have standards, you can also use Triple quad.