I seem to keep googling this. … and this is not final and magic and I should actually understand this on a deeper level.

Not today.

So.

TL;DR for copypaste

Reading lines in a file:

while IFS="" read -r p || [ -n "$p" ]
do
  printf '%s\n' "$p"
done < peptides.txt

For outputs of a command:

while read -r p; do
	echo $p;
done < <(echo "one\ntwo")

Easy option with cat

Otherwise: Easy option that I can memorize, both for lines in command and in file that will will skip the last line if it doesn’t have a trailing newline:

for word in $(cat peptides.txt); do echo $word; done

Same idea but with avoiding this bug:

cat peptides.txt | while read line || [[ -n $line ]];
do
   # do something with $line here
done

Correct option without cat

1. Same as first cat option above, same drawbacks, but no use of cat:

   while read p; do
     echo "$p"
   done <peptides.txt
   

2. Same as above but without the drawbacks:

   while IFS="" read -r p || [ -n "$p" ]
   do
     printf '%s\n' "$p"
   done < peptides.txt
   

3. This would make command read from stdin, 10 is arbitrary:

   while read -u 10 p; do
     ...
   done 10<peptides.txt
   

(All this from the same SO answer¹).

In general, if you’re using “cat” with only one argument, you’re doing something wrong (or suboptimal).