"The bus doesn't work" is not a bug report a logic analyzer can answer by itself, and the gap between clipping on four wires and actually learning something is where most of a session goes. Lab Equipment and What It Answers makes the case for reaching for the analyzer first and works one I²C bug through it end to end; this page assumes you have already made that choice and is about running the capture well enough that the answer it gives you is true.
Below the level of PCIe and USB, most chip-to-chip communication on a circuit board — a sensor
SPI is a shift register with a wire between two halves of it. That is the whole protocol, and holding it in mind explains everything the peripheral does. The controller has eight bits, the target has eight bits, and the clock the controller generates walks them past each other in a ring: the controller's MSB goes out on MOSI and into the target's LSB position, the target's MSB goes out on MISO and into the controller's. After eight clocks the two registers have swapped contents. There is no addressing, no acknowledgement, no error detection and no notion of a transaction — every one of those has to be built on top by whatever protocol the target's datasheet defines.