Mass spectrometry — common mistakes

Do not confuse the molecular ion peak with the base peak. The molecular ion peak is the one with the highest $m/z$ value. The base peak is the tallest peak in the spectrum, representing the most abundant (and often most stable) fragment. They can be the same, but often are not.

During electron impact ionisation, it requires a certain amount of energy to remove one electron. Removing a second electron from an already positive ion requires significantly more energy. While it is possible to form +2 or +3 ions, it is far less likely. Therefore, the vast majority of ions detected have a +1 charge.

Yes, often it can. Structural isomers have the same molecular formula and therefore the same relative molecular mass, so they will have the same molecular ion peak ($M^+$). However, they have different structures and bond arrangements, so they tend to break apart (fragment) in different ways. This leads to different fragmentation patterns, with different peaks and/or different relative abundances, allowing them to be distinguished.

Electrospray ionisation is a 'softer' ionisation technique. The sample is dissolved in a volatile solvent and sprayed through a fine, high-voltage needle. This creates charged droplets, and as the solvent evaporates, ions are formed (typically $[M+H]^+$). ESI is much less energetic than EI and causes little to no fragmentation. It is useful for finding the $M_r$ of large, fragile molecules like proteins that would be destroyed by electron impact.