page update

notes/20241001_FI.md

@@ -76,13 +76,13 @@ can be avoided for all subsequent files being searched.
   might further be limited by the total allowed number of modified residues
   in a peptide controlled by the [max_variable_mods_in_peptide](https://uwpr.github.io/Comet/parameters/parameters_202402/max_variable_mods_in_peptide.html) parameter.
 
-### Fragmen ion index specific search parameters
-- fragindex_min_ions_score  some documentation coming
-- fragindex_min_ions_report
-- fragindex_num_spectrumpeaks
-- fragindex_min_fragmentmass
-- fragindex_max_fragmentmasss
-- fragindex_skipreadprecursors
+### Fragment ion index specific search parameters
+- [fragindex_min_fragmentmass](/Comet/parameters/parameters_202402/fragindex_min_fragmentmass.html)
+- [fragindex_max_fragmentmasss](/Comet/parameters/parameters_202402/fragindex_max_fragmentmass.html)
+- [fragindex_min_ions_report](/Comet/parameters/parameters_202402/fragindex_min_ions_report.html)
+- [fragindex_min_ions_score](/Comet/parameters/parameters_202402/fragindex_min_ions_score.html)
+- [fragindex_num_spectrumpeaks](/Comet/parameters/parameters_202402/fragindex_num_spectrumpeaks.html)
+- [fragindex_skipreadprecursors](/Comet/parameters/parameters_202402/fragindex_skipreadprecursors.html)
 
 ### Memory use performance
 
@@ -94,11 +94,12 @@ There are many factors that go into how much memory will be consumed including:
 - mass range of the fragment ions used in the index
 
 I will simply state that one can easily generate over a billion fragment ions in
-a standard analysis.  And representing a billion fragment ions in a fragment index
+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 32GB machine.  Many searches can be done on a 64GB box.  And if you're a power
-user who wants to analyze MHC peptides requiring no-enzyme searches, make sure you
-have a 128GB box before attempting this analysis with this version of Comet.
+user who wants to analyze MHC peptides requiring non-specific enzyme constraint searches,
+make sure you have a 128GB box before attempting this analysis with this version of Comet.
 
 The following searches were run using 8-cores of an AMD Epyc 7443P processor with
 256GB RAM running on Ubuntu linux version 22.04  Search times and memory use are 

notes/index.md

@@ -17,7 +17,7 @@ ms2/cms2 formats and a comet.params file.  Then issue a command such as:
 
 ### Miscellaneous Notes
 
-- 2024/10/01:  [Comet fragmention index](20241001_FI.html)
+- 2024/10/01:  [Comet fragment ion index](20241001_FI.html)
 - 2023/06/13:  [Linux compile issues](20230613_linuxcompile.html)
 - 2022/02/28:  [Searching Thermo RAW files supported only under Windows](20220228_rawfile.html)
 - 2020/12/01:  [Terminal modification masses](20201201_terminalmods.html)

releases/release_202402.md

@@ -6,26 +6,28 @@ Download release [here](https://github.com/UWPR/Comet/releases).
 
 #### release 2024.02 rev. 0 (2024.02.0), release date 2024/10/14
 
-- This is the first release to official support fragment ion indexing, which
-is a method that was originally implemented by [MSFragger](https://msfragger.nesvilab.org/) in 2017.
+- Add fragment ion indexing support.
+While fragment ion indexing code was present in the 2024.01 rev. 0 release, 
+this is the first release to official support fragment ion indexing, which
+is a method that was originally implemented by [MSFragger](https://www.nature.com/articles/nmeth.4256).
 In Comet's implementation, the fragment ion index is applied as a
-candidate peptide filter prior to performing full cross-correlation scoring.
+candidate peptide filter prior to performing full cross-correlation analysis.
 [Please see this note](https://uwpr.github.io/Comet/notes/20241001_FI.html)
-for more details on Comet's fragment ion index. The following are
-new search parameters specific to this feature.
+for more details on Comet's fragment ion index.
 Thanks to V. Sharma for implementing the modifications permutation code and
 to E. Bergstrom, C. McGann, and D. Schweppe for driving the development and testing.
-  - Added [fragindex_max_fragmentmass](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_max_fragmentmass.html)
-  - Added [fragindex_min_fragmentmass](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_fragmentmass.html)
-  - Added [fragindex_min_ions_report](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_ions_report.html)
-  - Added [fragindex_min_ions_score](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_ions_score.html)
-  - Added [fragindex_num_spectrumpeaks](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_num_spectrumpeaks.html)
-  - Added [fragindex_skipreadprecursors](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_skipreadprecursors.html)
+The following are new search parameters specific to this feature.
+  - [fragindex_max_fragmentmass](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_max_fragmentmass.html)
+  - [fragindex_min_fragmentmass](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_fragmentmass.html)
+  - [fragindex_min_ions_report](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_ions_report.html)
+  - [fragindex_min_ions_score](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_ions_score.html)
+  - [fragindex_num_spectrumpeaks](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_num_spectrumpeaks.html)
+  - [fragindex_skipreadprecursors](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_skipreadprecursors.html)
 
 - Allow variable modifications to apply to a subet of proteins.
-For example, one can apply mono-, di-, and tri-methylation
-variable modifications to only histone proteins and not all
-human proteins in the database. This functionality is controlled by the
+For example, one can now apply mono-, di-, and tri-methylation
+as variable modifications to only histone proteins and not all
+proteins in the human database. This functionality is controlled by the
 [protein_modlist_file](https://uwpr.github.io/Comet/parameters/parameters_202402/protein_modlist_file.html)
-parameter.  Note there will be issues for FDR analysis with
-when applying this feature.  Feature requested by C. McGann.
+parameter.  Note there will be issues for post processing analysis, such
+as FDR, when applying this feature.  Thanks to C. McGann for the feature request.