update params

parameters/parameters_202402/fragindex_max_fragmentmass.md

@@ -1,6 +1,8 @@
 ### Comet parameter: fragindex_max_fragmentmass
 
-- Documentation.
+- This parameter defines the maximum fragment ion mass to include in the fragment ion index
+- The mass is the singly charged fragment mass.
+- Valid values are a positive decimal number.
 
 Example:
 ```

parameters/parameters_202402/fragindex_min_fragmentmass.md

@@ -1,6 +1,8 @@
 ### Comet parameter: fragindex_min_fragmentmass
 
-- Documentation.
+- This parameter defines the minimum fragment ion mass to include in the fragment ion index
+- The mass is the singly charged fragment mass.
+- Valid values are a positive decimal number.
 
 Example:
 ```

parameters/parameters_202402/fragindex_min_ions_report.md

@@ -1,6 +1,13 @@
 ### Comet parameter: fragindex_min_ions_report
 
-- Documentation.
+- This parameter sets the minimum number fragment ions a peptide must match
+  against the fragment ion index in order to report this peptide in the output.
+- This parameter value could be different (typically same or larger) than the
+  [fragindex_min_ions_score](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_ions_score.html)
+  parameter.
+- Any peptide that passes this filter is a candidate to be reported in the output
+  list, assuming it scores high enough.
+- Valid values are integers, 1 or larger.
 
 Example:
 ```

parameters/parameters_202402/fragindex_min_ions_score.md

@@ -1,6 +1,16 @@
 ### Comet parameter: fragindex_min_ions_score
 
-- Documentation.
+- This parameter sets the minimum number fragment ions a peptide must match
+  against the fragment ion index in order to proceed to xcorr scoring.
+- This parameter could be different (typically same or larger) than the
+  [fragindex_min_ions_report](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_ions_report.html)
+  parameter.
+- This parameter is intended to allow more candidate peptides to be scored, thus
+  filling out the xcorr score histogram for a better E-value calculation.
+  However, only peptides that pass the
+  [fragindex_min_ions_report](https://uwpr.github.io/Comet/parameters/parameters_202402/fragindex_min_ions_report.html)
+  filter will be reported in the output list.  
+- Valid values are integers, 1 or larger.
 
 Example:
 ```

parameters/parameters_202402/fragindex_num_spectrumpeaks.md

@@ -1,6 +1,11 @@
 ### Comet parameter: fragindex_num_spectrumpeaks
 
-- Documentation.
+- This parameter defines the number of mass/intensity pairs query against the
+  fragment ion index.
+- Raw peaks from the query spectrum are stored, starting from the most intense peak.
+- The larger this value is set, the slower a search will be as each additional
+  peak will need to be queried against the fragment ion index.
+- Valid value is a positive integer.
 
 Example:
 ```

parameters/parameters_202402/fragindex_skipreadprecursors.md

@@ -1,6 +1,13 @@
 ### Comet parameter: fragindex_skipreadprecursors
 
-- Documentation.
+- This parameter controls whether or not Comet reads all precursors from the
+  input files.  It usees this information to limit the peptides that
+  are included in the fragment ion index.
+- Typically it is advantageous to apply this parameter. However, for some
+  large input files with many MS/MS spectra, parsing all precursors can take
+  time and may not provide a meaningful reduction in the fragment ion index.
+- 0 = skip reading precursors from the input ifle
+- 1 = read precursors from the input file
 
 Example:
 ```