Update 20241001_FI.md

Author: jke000

notes/20241001_FI.md

@@ -7,7 +7,7 @@ to go use MSFragger, MetaMorpheus, Sage and all of the other great peptide ident
 tools out there.
 
 Fragment ion indexing (abbreviated as "FI" or "Comet-FI" going forward) is supported 
-n Comet as of [version 2024.02 rev. 0](https://uwpr.github.io/Comet/releases/release_202402.html).
+in Comet as of [version 2024.02 rev. 0](https://uwpr.github.io/Comet/releases/release_202402.html).
 Given this is the first Comet release with FI functionality, we expect to improve on
 features, performance, and functionality going forward.
 
@@ -109,7 +109,7 @@ multiple variable modifications).
 - [fragindex_num_spectrumpeaks](/Comet/parameters/parameters_202402/fragindex_num_spectrumpeaks.html)
 - [fragindex_skipreadprecursors](/Comet/parameters/parameters_202402/fragindex_skipreadprecursors.html)
 
-### Memory use performance
+### Memory use and performance
 
 There are many factors that go into how much memory will be consumed including:
 - database size
@@ -118,10 +118,10 @@ There are many factors that go into how much memory will be consumed including:
 - number of variable modifications considered
 - mass range of the fragment ions used in the index
 
-One can easily generate over a billion fragment ions in
-a standard human, target + decoy, tryptic analysis by adding a few variable modifications.
-And representing a billion fragment ions in a fragment index
-in memory will require many GBs of RAM.  You might get away with some smaller searches
+One can easily generate over a billion fragment ions in a standard human,
+target + decoy, tryptic analysis by adding a few variable modifications.
+And representing a billion fragment ions in a fragment index in memory will
+require many GBs of RAM.  You might get away with some smaller searches
 on a 16 GB or 32 GB machine.  Many searches can be done with 64 GB RAM.  And if you're a power
 user who wants to analyze MHC peptides requiring non-specific enzyme constraint searches,
 don't attempt to run such a search with many modifications as it simply won't work.
@@ -137,7 +137,8 @@ The .idx files were created before the search so the reported search times and
 
 - Yeast forward + reverse (12,488 sequence entries), 
   variable mods 16M and 80STY uses 5.6 GB of RAM and
-  completes in 0:30.  The .idx creation step took 0:03 to complete.
+  completes in 0:30.  The plain peptide .idx file
+  creation step took 0:03 to complete.
 - Human forward + reverse (193,864 sequence entries),
   variable mods 16M uses 5.2 GB of RAM and completes in 0:31.
   During the search, populating the fragment ion index took