The method isProtected() does not exist on PhpParser\Node. It seems like you code against a sub-type of PhpParser\Node such as PhpParser\Node\Stmt\Property or PhpParser\Node\Stmt\ClassMethod or PhpParser\Node\Stmt\ClassConst or PhpParser\Node\Stmt\ClassMethod.
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Ignorable by Annotation
)
If this is a false-positive, you can also ignore this issue in your code via the ignore-call annotation
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if ($node->/** @scrutinizer ignore-call */ isProtected()) {