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Update the parameter files.
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@fcyu
fcyu committed Dec 19, 2023
1 parent 424ebea commit 8f2a6d3
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Showing 4 changed files with 8 additions and 12 deletions.
5 changes: 2 additions & 3 deletions parameter_files/Nglyco-HCD_fragger.params
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@@ -1,11 +1,11 @@
# MSFragger-3.8
# MSFragger-4.0
num_threads = 0 # Number of CPU threads to use.
database_name = test.fasta # Path to the protein database file in FASTA format.

precursor_mass_lower = -20 # Lower bound of the precursor mass window.
precursor_mass_upper = 20 # Upper bound of the precursor mass window.
precursor_mass_units = 1 # Precursor mass tolerance units (0 for Da, 1 for ppm).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window, 3 for DDA+).
precursor_true_tolerance = 20 # True precursor mass tolerance (window is +/- this value).
precursor_true_units = 1 # True precursor mass tolerance units (0 for Da, 1 for ppm).
fragment_mass_tolerance = 20 # Fragment mass tolerance (window is +/- this value).
Expand Down Expand Up @@ -79,7 +79,6 @@ track_zero_topN = 0 # Track top N unmodified peptide res
# set to a number greater than output_report_topN if zero bin boosting is desired.
zero_bin_accept_expect = 0.00 # Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value.
zero_bin_mult_expect = 1.00 # Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting).
add_topN_complementary = 0 # Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectra.

check_spectral_files = 1 # Checking spectral files before searching.
minimum_peaks = 15 # Minimum number of peaks in experimental spectrum for matching.
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5 changes: 2 additions & 3 deletions parameter_files/closed_fragger.params
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
# MSFragger-3.8
# MSFragger-4.0
num_threads = 0 # Number of CPU threads to use.
database_name = test.fasta # Path to the protein database file in FASTA format.

precursor_mass_lower = -20 # Lower bound of the precursor mass window.
precursor_mass_upper = 20 # Upper bound of the precursor mass window.
precursor_mass_units = 1 # Precursor mass tolerance units (0 for Da, 1 for ppm).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window, 3 for DDA+).
precursor_true_tolerance = 20 # True precursor mass tolerance (window is +/- this value).
precursor_true_units = 1 # True precursor mass tolerance units (0 for Da, 1 for ppm).
fragment_mass_tolerance = 20 # Fragment mass tolerance (window is +/- this value).
Expand Down Expand Up @@ -76,7 +76,6 @@ track_zero_topN = 0 # Track top N unmodified peptide res
# set to a number greater than output_report_topN if zero bin boosting is desired.
zero_bin_accept_expect = 0.00 # Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value.
zero_bin_mult_expect = 1.00 # Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting).
add_topN_complementary = 0 # Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectra.

check_spectral_files = 1 # Checking spectral files before searching.
minimum_peaks = 15 # Minimum number of peaks in experimental spectrum for matching.
Expand Down
5 changes: 2 additions & 3 deletions parameter_files/nonspecific_fragger.params
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
# MSFragger-3.8
# MSFragger-4.0
num_threads = 0 # Number of CPU threads to use.
database_name = test.fasta # Path to the protein database file in FASTA format.

precursor_mass_lower = -20 # Lower bound of the precursor mass window.
precursor_mass_upper = 20 # Upper bound of the precursor mass window.
precursor_mass_units = 1 # Precursor mass tolerance units (0 for Da, 1 for ppm).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window, 3 for DDA+).
precursor_true_tolerance = 20 # True precursor mass tolerance (window is +/- this value).
precursor_true_units = 1 # True precursor mass tolerance units (0 for Da, 1 for ppm).
fragment_mass_tolerance = 20 # Fragment mass tolerance (window is +/- this value).
Expand Down Expand Up @@ -76,7 +76,6 @@ track_zero_topN = 0 # Track top N unmodified peptide res
# set to a number greater than output_report_topN if zero bin boosting is desired.
zero_bin_accept_expect = 0.00 # Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value.
zero_bin_mult_expect = 1.00 # Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting).
add_topN_complementary = 0 # Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectra.

check_spectral_files = 1 # Checking spectral files before searching.
minimum_peaks = 15 # Minimum number of peaks in experimental spectrum for matching.
Expand Down
5 changes: 2 additions & 3 deletions parameter_files/open_fragger.params
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
# MSFragger-3.8
# MSFragger-4.0
num_threads = 0 # Number of CPU threads to use.
database_name = test.fasta # Path to the protein database file in FASTA format.

precursor_mass_lower = -150 # Lower bound of the precursor mass window.
precursor_mass_upper = 500 # Upper bound of the precursor mass window.
precursor_mass_units = 0 # Precursor mass tolerance units (0 for Da, 1 for ppm).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window).
data_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window, 3 for DDA+).
precursor_true_tolerance = 20 # True precursor mass tolerance (window is +/- this value).
precursor_true_units = 1 # True precursor mass tolerance units (0 for Da, 1 for ppm).
fragment_mass_tolerance = 20 # Fragment mass tolerance (window is +/- this value).
Expand Down Expand Up @@ -76,7 +76,6 @@ track_zero_topN = 0 # Track top N unmodified peptide res
# set to a number greater than output_report_topN if zero bin boosting is desired.
zero_bin_accept_expect = 0.00 # Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value.
zero_bin_mult_expect = 1.00 # Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting).
add_topN_complementary = 0 # Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectra.

check_spectral_files = 1 # Checking spectral files before searching.
minimum_peaks = 15 # Minimum number of peaks in experimental spectrum for matching.
Expand Down

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