So what I'm seeing is that your opening parenthesis/bracket is preceeded by a space -- if you look for that space and then the punctuation, maybe that will help?

So like something like this??

def extract_main_protein_name(name):
    """
    Extract the main protein name by removing descriptive parentheses/brackets
    while preserving functional ones (like ion charges).
    """
    # Remove descriptive content in parentheses/brackets that are preceded by a space
    # This regex looks for white space followed by an opening bracket/parenthesis, then removes everything until the end
    pattern = r'\s+[\(\[].*'
    cleaned_name = re.sub(pattern, '', name).strip()
    return cleaned_name

# Apply the function to clean protein names
df['Protein names'] = df['Protein names'].apply(extract_main_protein_name)