Why does my guitar sound more natural when plugged directly into a tube amp vs through a pedal board?
Why does my guitar sound better when plugged straight in to my amplifier as opposed to running it through a pedalboard without a true bypass strip?
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Often it's because of low quality cables and jumpers. There's also the fact that many pedals, when bypassed, still route the signal through the circuitry, which degrades the signal. Here's an article about true bypass and buffers that I think will answer some of your questions.
There are many factors that can cause the loss of frequency response problem.
Long cable runs can affect frequency response if the cables are not good quality. The longer the cable, the more resistance, capacitance and/or impedance can kick in and mess with the signal.
Dirty plugs/jacks/volume pots can cause problems too.
Chains of effects, or poorly built effects can do it.
You can attack the problem several ways.
Wireless transmitters remove the cable from the equation entirely, but can add additional problems, so you have to balance the pros and cons.
Super-high quality cables can help retain highs by reducing capacitance.
Adding active electronics, or a little high-quality op-amp into the guitar can bump up your sound output, getting it sufficiently high above the noise so all your signal remains clean. It could also reduce your impedance, while maintaining high output, and keep a very clean signal. I used to add little op-amps to my Strats, to keep that nice sparkly sound while giving them a tiny bit more output signal.
Reduce your cable runs to the bare minimum. If you have coils of cable between you and the amp or effects, you have too much. Remember that a coiled cable might appear to keep the length short, because it contracts, but it remains its full 20' length, even when contracted to 5'. I have short cords of 5' and 10' to let me customize based on my needs on a stage or studio or at home practicing.
Basically, your best sound will always be straight into the amp with the shortest high quality cable length available. Anything in the way has potential to mess with the signal.
When the guitar tries to feed a signal to some other device, the other device will, in a sense, "push back". A measure called "impedance" describes, at any given frequency, both the behavior of the input, which is "pushing back", and the signal source (which may respond to that "push-back" by pushing somewhat harder itself). The construction of some devices will cause them exhibit impedance which varies in "interesting" ways with frequency. Many modern electronic input and output stages, however, are designed to have impedance characteristics which are relatively uniform. If a guitar pickup with "interesting" impedance characteristics is passed into an amplifier which also has "interesting" impedance characteristics, the pickup and the amplifier may interact in "interesting" ways which would not occur with a guitar pickup that was driving a pedal input stage which has uniform impedance, nor when a uniform-impedance pedal output was driving an "interesting" amplifier input stage.
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