params update

parameters/parameters_202402/fragindex_max_fragmentmass.md

@@ -1,10 +1,18 @@
 ### Comet parameter: fragindex_max_fragmentmass
 
-- This parameter defines the maximum fragment ion mass to include in the fragment ion index
+- This parameter defines the maximum fragment ion mass to include
+  in the fragment ion index.
 - The mass is the singly charged fragment mass.
+- A smaller value will use less memory and generate the fragment ion
+  index faster as less fragment ions will be added to the index.
+- Specifying too small a value may remove fragment ions
+  from consideration that would otherwise aid in peptides passing the
+  fragment ion index filter.
+- If this value is not specified, the default value is 2000.0.
 - Valid values are a positive decimal number.
 
 Example:
 ```
 fragindex_max_fragmentmass = 1500.0
+fragindex_max_fragmentmass = 2000.0
 ```

parameters/parameters_202402/fragindex_min_fragmentmass.md

@@ -1,7 +1,14 @@
 ### Comet parameter: fragindex_min_fragmentmass
 
-- This parameter defines the minimum fragment ion mass to include in the fragment ion index
+- This parameter defines the minimum fragment ion mass to include
+  in the fragment ion index.
 - The mass is the singly charged fragment mass.
+- A larger value will use less memory and generate the fragment ion
+  index faster as less fragment ions will be added to the index.
+- Specifying too large a value may remove fragment ions
+  from consideration that would otherwise aid in peptides passing
+  the fragment ion index filter.
+- If this value is not specified, the default value is 200.0.
 - Valid values are a positive decimal number.
 
 Example:

parameters/parameters_202402/fragindex_min_ions_report.md

@@ -3,11 +3,11 @@
 - 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)
+  [fragindex_min_ions_score](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.
+- Valid values are a positive integer, 1 or larger.
 
 Example:
 ```

parameters/parameters_202402/fragindex_min_ions_score.md

@@ -3,14 +3,14 @@
 - 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)
+  [fragindex_min_ions_report](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)
+  [fragindex_min_ions_report](fragindex_min_ions_report.html)
   filter will be reported in the output list.  
-- Valid values are integers, 1 or larger.
+- Valid values are a positive integer, 1 or larger.
 
 Example:
 ```

parameters/parameters_202402/fragindex_num_spectrumpeaks.md

@@ -1,13 +1,21 @@
 ### Comet parameter: fragindex_num_spectrumpeaks
 
-- This parameter defines the number of mass/intensity pairs query against the
+- This parameter defines the number of mass/intensity pairs that would be
+  queried against the fragment ion index.
+- Raw peaks are parsed and stored. The mass dimension is binned per the
+  [fragment_bin_tol](fragment_bin_tol.html) and the most intense binned peaks
+  are used to query the fragment ion index.
+- The larger this value is, the slower a search will be as each additional
+  peak, from every query spectra, will need to be searched 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.
+- Note that specifying too small a value can be detrimental as, for some
+  spectra, correct peptides may not pass the fragment ion index filter
+  if there are not enough peaks queried.
+- Valid values are integers, 1 or larger.
 
 Example:
 ```
 fragindex_num_spectrumpeaks = 100
+fragindex_num_spectrumpeaks = 150
+fragindex_num_spectrumpeaks = 200
 ```

parameters/parameters_202402/fragindex_skipreadprecursors.md

@@ -1,11 +1,19 @@
 ### Comet parameter: fragindex_skipreadprecursors
 
 - 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.
+  input files.  It uses this information to limit the peptides that
+  are included in the fragment ion index.  Otherwise, every peptides within
+  the mass range defined by [digest_mass_range](digest_mass_range.html)
+  will be included in the fragment ion index (even though only those
+  with precursor masses corresponding to experimental spectra would be
+  used in the analysis).
+- This parameter is meant to reduce the fragment ion index size, saving
+  both memory use and run time in generating the 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.
+  a lot of time and may not provide a meaningful reduction in the fragment
+  ion index.
+- Valid values are 0 or 1.
 - 0 = skip reading precursors from the input ifle
 - 1 = read precursors from the input file
 

parameters/parameters_202402/output_txtfile.md

@@ -85,3 +85,27 @@ scan  charge   spectrum precursor m/z  spectrum neutral mass   peptide mass   de
 5165  3  432.885100  1295.633471 1294.628231 0.5551   70.6711  42 1.0112   5  11 40 917   QALEEKASALR R.QALEEKAS[79.9663]ALR.T   8_V_79.966331  sp|A0A096LP49|CC187_HUMAN  RT 2.11E+01
 
 ```
+
+Here's a description of each column in the regular Comet (non-Crux) output:
+
+- scan:  The scan number of the spectrum that was searched.
+- num:  For each scan, the top N best scoring peptides are returned, controlled by the [num_output_lines](num_output_lines.html) parameter.  This column displays the peptide order for each scan, starting at "1" to indicate the top scoring peptide, "2" to indicate the second best scoring peptide, etc.
+- charge:  The precursor charge state
+- exp_neutral_mass:  The experimental neutral mass of the measured precursor ion.
+- calc_neutral_mass:  The calculated neutral mass of the matched peptide.
+- e_value:  The expectation value or E-value score for the peptide.  See this paper for some info on [how Comet calculates E-values](https://pubs.acs.org/doi/10.1021/pr800420s) (although there is a correction where the log transform of the cumulative xcorr distribution is used instead of the log transform of the xcorr histogram).
+- xcorr:  The cross correlation score for the peptide.  [Here's a very nice illustration](https://willfondrie.com/2019/02/an-intuitive-look-at-the-xcorr-score-function-in-proteomics/) of how this score is calculated by Will Fondrie.
+- delta_cn:  The deltaCn which is the difference in the normalized cross correlation score, historically between top hit and next best hit.  In Comet, each deltaCn score for each row is the  difference in the normalized cross correlation score between that hit and next lower peptide hit.
+- sp_score:  The preliminary score which is the sum of peak intensities that match the peptide and accounts for continuity of an ion series and the length of the peptide.  I think of this as a quick/simple peptide match score that now exists only for backwards compatibility for post-search processing tools.
+- ions_matched:  Out of the total number of theoretical fragment ions being considered in the search, this is the number of those ions that were found in the experimental spectrum.
+- ions_total:   The total number of theoretical fragment ions for the peptide.
+- plain_peptide:  The raw peptide sequence.
+- modified_peptide:  The peptide sequence including previous and next amino acids as well as any variable modifications.
+- prev_aa:  In the first protein that contains this peptide, the amino acid just before or n-terminal to the peptide.
+- next_aa:   In the first protein that contains this peptide, the amino acid just after or c-terminal to the peptide.
+- protein:  A comma separated list of proteins that contain the identified peptide. The maximum number of proteins printed out is controlled by the [max_duplicate_proteins](max_duplicate_proteins.html) parameter.
+- protein_count:  The total number of proteins in the database that contains the peptide.
+- modifications:  An encoding of static and variable modifications in the peptide as described above.
+- retention_time_sec:  If available from the query file, this reports the retention time in seconds of the spectrum being searched.
+- sp_rank:  The rank of the preliminary score (Sp).  If the peptide results were ordered by the sp_score column, this column reports the rank order of this peptide when sorted by sp_score.  So if this peptide had the fourth highest sp_score, this column would contain a "4".
+