I would like to know your experiences with these type of microorganisms detection and if you used more than one, which one you would recommend and why?
Your post is unclear and can not be easily answered. Please identify your actual question(s), state your scientific goals and provide some background with what you are trying to learn or obtain. The better the job you do in articulating a question(s), the more likely you are to get relevant responses.
You ask about "Light-scattering". Are you aware of the fact that many different types of light-scattering detectors, systems and techniques exist? All of them different and all with different purposes or functionality in mind.
PCR is more specific and applicable to many organisms. Its applicability depends on what question you have and if there is PCR data to compare your sample too.
Maldi TOF Mass Spec is a technique. First, you would need to describe what you wish to determine and then establish if the technique is applicable for your sample types as well as do you have the resources to prep the samples, develop the method(s), run the needed samples and have the results interpreted.
I have experience with MALDI-TOF MS to do bacterial and fungal identification and classification with good results. Our group also work with qPCR to do microrganism identification and MALDI-TOF method is easier, faster and cheaper than qPCR. The great point with MALDI-TOF is that you shall use a reference spectra database to confidently identify your samples. If you need more specific information about MALDI-TOF to do microrganism identification please ask.
What 3 microorganisms do you have in mind? Think MALDI-TOF MS is used for identification - not detection ,and Spartan Cube is so new, doubt many have enough experience to relate.