From 13496fe29e437cfe37d634af863ee2c4d45305d3 Mon Sep 17 00:00:00 2001 From: jke000 Date: Fri, 4 Oct 2024 17:03:07 -0700 Subject: [PATCH] update params --- .../parameters_202402/fragindex_max_fragmentmass.md | 4 +++- .../parameters_202402/fragindex_min_fragmentmass.md | 4 +++- .../parameters_202402/fragindex_min_ions_report.md | 9 ++++++++- .../parameters_202402/fragindex_min_ions_score.md | 12 +++++++++++- .../parameters_202402/fragindex_num_spectrumpeaks.md | 7 ++++++- .../fragindex_skipreadprecursors.md | 9 ++++++++- 6 files changed, 39 insertions(+), 6 deletions(-) diff --git a/parameters/parameters_202402/fragindex_max_fragmentmass.md b/parameters/parameters_202402/fragindex_max_fragmentmass.md index 5a9e1d7d..fc82c612 100644 --- a/parameters/parameters_202402/fragindex_max_fragmentmass.md +++ b/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: ``` diff --git a/parameters/parameters_202402/fragindex_min_fragmentmass.md b/parameters/parameters_202402/fragindex_min_fragmentmass.md index 4dfb5d98..a4e3768a 100644 --- a/parameters/parameters_202402/fragindex_min_fragmentmass.md +++ b/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: ``` diff --git a/parameters/parameters_202402/fragindex_min_ions_report.md b/parameters/parameters_202402/fragindex_min_ions_report.md index b139cb00..28102b16 100644 --- a/parameters/parameters_202402/fragindex_min_ions_report.md +++ b/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: ``` diff --git a/parameters/parameters_202402/fragindex_min_ions_score.md b/parameters/parameters_202402/fragindex_min_ions_score.md index ca90d88c..1156d69e 100644 --- a/parameters/parameters_202402/fragindex_min_ions_score.md +++ b/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: ``` diff --git a/parameters/parameters_202402/fragindex_num_spectrumpeaks.md b/parameters/parameters_202402/fragindex_num_spectrumpeaks.md index 113b1fdf..36c84604 100644 --- a/parameters/parameters_202402/fragindex_num_spectrumpeaks.md +++ b/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: ``` diff --git a/parameters/parameters_202402/fragindex_skipreadprecursors.md b/parameters/parameters_202402/fragindex_skipreadprecursors.md index 9fc17c56..24b96c5b 100644 --- a/parameters/parameters_202402/fragindex_skipreadprecursors.md +++ b/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: ```