When strumming muted strings, I'm getting more of a high-pitched metallic sound. How can I get a cleaner muted sound (such as in the main riff in Can't Stop by RHCP or Smells Like Teen Spirit). More gain seems to help but I can't quite get there. I'm a new player, so it could be my technique. 

I'm using a Fender Stratocaster and a Fender Champion 20 amp

It probably is more your technique than your gear.

Thread was moved to forum: Guitar Techniques
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It sounds like you might be putting a little too much pressure on the strings you're muting with your fretting hand. It doesn't take much pressure at all from your fretting hand to dampen the strings enough to perform the technique, just enough to stop the strings from vibrating.

For instance, to get that signature "chicka chicka" in Teen Spirit you'll actually want a lighter touch, probably with both your fret hand that's muting the strings and your pick hand - as too strong and tense of an approach with your picking hand during strings mutes like these can start to make your "chicka chicka" sound a little "chugga chugga", especially if your tone is perhaps a little too thick on the bottom.

Try playing these riffs you mentioned with a looser wrist and overall a slightly lighter touch. One fairly common issue for newer players is playing with too much force and tension in the picking hand, especially if you're the type who likes to drag an electric into the living room and run through scales and licks while you're watching TV or something, as it's natural and nearly second nature to start to pick a little harder than necessary to get the notes to project a little more when you're unplugged. Take a little time to strum out some riffs and play some licks with varying degrees of force from your picking hand and notice (a) how it doesn't really take that much force to get a note to ring out nicely and (b) how the strength of the pick approach affects each note.

Your issue is probably related to technique rather than tone, but its good to learn early on that probably need a bit less gain and bass than you think. Even though dialing in a little low end can help beef up the sound of a single coil, there's a point where the tone becomes muddy. Try backing off your lows to halfway up the knob, at most, maybe a little less. It's also a common mistake for newer players to dial in loads of unneeded gain - it happens to all of us at some point (and fwiw some unfortunately never outgrow it).
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Sounds like you're probably muting in a straight line too close to a harmonic node, which means you're getting at least some partial harmonics in with your muting. Try shifting your hand up and down the neck a bit to see how the sound changes.
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