page update

Author: jke000

notes/20241001_FI.md

@@ -111,21 +111,21 @@ make sure you have a 128GB box before attempting this analysis with this version
 The following searches were run using 8-cores of an AMD Epyc 7443P processor with
 256GB RAM running on Ubuntu linux version 22.04  Up to two of each specified variable
 modifications are allowed in a peptide.  The query file is a two hour Orbitrap Lumos
-run with MS/MS spectra acquired in the Orbitrap.  Peptide length 7 to 50 and
-digest mass range 600.0 to 5000.0.
+run with MS/MS spectra acquired in the Orbitrap.  Peptide length 7 to 50,
+digest mass range 600.0 to 5000.0, and tryptic digest with 2 allowed missed cleavages.
 
-- Yeast forward + reverse (12,488 sequence entries), tryptic, 1 allowed
-  missed cleavage, variable mods 16M and 80STY uses 5.6 GB of RAM and
+- Yeast forward + reverse (12,488 sequence entries), 
+  variable mods 16M and 80STY uses 5.6 GB of RAM and
   completes in 31 seconds.
-- Human forward + reverse (193,864 sequence entries), tryptic, 1 allowed
-  missed cleavage, variable mods 16M uses 5.2 GB of RAM and completes in
-  31 seconds.
-- Human forward + reverse (1XX,XXX sequence entries), tryptic, 1 allowed
-  missed cleavage, variable mods 16M, 80STY uses 11.3 GB of RAM and
+- Human forward + reverse (193,864 sequence entries),
+  variable mods 16M uses 5.2 GB of RAM and completes in 31 seconds.
+- Human forward + reverse, tryptic,
+  variable mods 16M, 80STY uses 11.3 GB of RAM and
   completes in 68 seconds.  Corresponding standard Comet search
   took 4 minutes and 10 seconds.
 - Human forward + reverse sequences, no enzyme constraint, 16M variable mod,
   peptide length range 7 to 15 uses 49 GB of RAM and completes in 5 minutes
-  and 30 seconds.  However, just creating the plain peptide .idx file takes
+  and 30 seconds.  Although performed once for every subsequent search,
+  it's notable that just creating the plain peptide .idx file takes
   over 100 GB RAM and 12 minutes.  The corresponding standard Comet search
   took 20 minutes and 5 seconds.