MSFraggerAdapter

Options

version

Version of the tool that generated this parameters file.

license

Set to yes, if you have read and agreed to the MSFragger license terms.

java_heapmemory

Maximum Java heap size (in MB)

reindex

Recalculate peptide to protein association using OpenMS. Annotates target-decoy information.

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

precursor_mass_tolerance_lower

Lower precursor mass tolerance

precursor_mass_tolerance_upper

Upper precursor mass tolerance

precursor_mass_unit

Unit of precursor mass tolerance

precursor_true_tolerance

True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches.

precursor_true_unit

Unit of precursor true tolerance

fragment_mass_tolerance

Fragment mass tolerance (window is +/- this value)

fragment_mass_unit

Unit of fragment mass tolerance

isotope_error

Isotope correction for MS/MS events triggered on isotopic peaks. Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12.

search_enzyme_name

Name of the enzyme to be written to the pepXML file

search_enzyme_cutafter

Residues after which the enzyme cuts (specified as a string of amino acids)

search_enzyme_nocutbefore

Residues that the enzyme will not cut before

num_enzyme_termini

Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)

allowed_missed_cleavage

Allowed number of missed cleavages

min_length

Minimum length of peptides to be generated during in-silico digestion

max_length

Maximum length of peptides to be generated during in-silico digestion

mass_range_min

Min mass of peptides to be generated (Da)

mass_range_max

Max mass of peptides to be generated (Da)

clip_nterm_m

Specifies the trimming of a protein N-terminal methionine as a variable modification

masses

Masses for variable modifications

syntaxes

Syntax Strings for variable modifications

unimod

Variable modifications in unimod syntax, is added to mass+syntax varmod list

enable_common

Enable common variable modifications (15.9949 M and 42.0106 [^)

not_allow_multiple_variable_mods_on_residue

Do not allow any one amino acid to be modified by multiple variable modifications

max_variable_mods_per_peptide

Maximum total number of variable modifications per peptide

max_variable_mods_combinations

Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534). If a greater number than the maximum is generated, only the unmodified peptide is considered

minimum_peaks

Minimum number of peaks in experimental spectrum for matching

use_topn_peaks

Pre-process experimental spectrum to only use top N peaks

minimum_ratio

Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity

clear_mz_range_min

Removes peaks in this m/z range prior to matching (minimum value). Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)

clear_mz_range_max

Removes peaks in this m/z range prior to matching (maximum value). Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)

max_fragment_charge

Maximum charge state for theoretical fragments to match

override_charge

Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)

precursor_charge_min

Min charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set)

precursor_charge_max

Max charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set)

track_zero_topn

Track top N unmodified peptide results separately from main results internally for boosting features. Should be set to a number greater than search:output_report_topN if zero bin boosting is desired

zero_bin_accept_expect

Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value

zero_bin_mult_expect

Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)

add_topn_complementary

Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum. Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option

min_fragments_modeling

Minimum number of matched peaks in PSM for inclusion in statistical modeling

min_matched_fragments

Minimum number of matched peaks for PSM to be reported. MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches

output_report_topn

Reports top N PSMs per input spectrum

output_max_expect

Suppresses reporting of PSM if top hit has expectation greater than this threshold

localize_delta_mass

Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)

add_cterm_peptide

Statically add mass in Da to C-terminal of peptide

add_nterm_peptide

Statically add mass in Da to N-terminal of peptide

add_cterm_protein

Statically add mass in Da to C-terminal of protein

add_nterm_protein

Statically add mass in Da to N-terminal of protein

add_G_glycine

Statically add mass to glycine

add_A_alanine

Statically add mass to alanine

add_S_serine

Statically add mass to serine

add_P_proline

Statically add mass to proline

add_V_valine

Statically add mass to valine

add_T_threonine

Statically add mass to threonine

add_C_cysteine

Statically add mass to cysteine

add_L_leucine

Statically add mass to leucine

add_I_isoleucine

Statically add mass to isoleucine

add_N_asparagine

Statically add mass to asparagine

add_D_aspartic_acid

Statically add mass to aspartic_acid

add_Q_glutamine

Statically add mass to glutamine

add_K_lysine

Statically add mass to lysine

add_E_glutamic_acid

Statically add mass to glutamic_acid

add_M_methionine

Statically add mass to methionine

add_H_histidine

Statically add mass to histidine

add_F_phenylalanine

Statically add mass to phenylalanine

add_R_arginine

Statically add mass to arginine

add_Y_tyrosine

Statically add mass to tyrosine

add_W_tryptophan

Statically add mass to tryptophan

unimod

Fixed modifications in unimod syntax if specific mass is unknown, e.g. Carbamidomethylation (C). When multiple different masses are given for one aminoacid this parameter (unimod) will have priority.

decoy_string

String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins. If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix).

decoy_string_position

Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession? (ignored if decoy_string is empty)

missing_decoy_action

Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)

write_protein_sequence

If set, the protein sequences are stored as well.

write_protein_description

If set, the protein description is stored as well.

keep_unreferenced_proteins

If set, protein hits which are not referenced by any peptide are kept.

unmatched_action

If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit.

aaa_max

Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs. AAAs are 'B', 'J', 'Z' and 'X'.

mismatches_max

Maximal number of mismatched (mm) amino acids allowed when matching to a protein database. The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's.

IL_equivalent

Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable). Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching.

allow_nterm_protein_cleavage

Allow the protein N-terminus amino acid to clip.

name

Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input

specificity

Specificity of the enzyme. Default: deduce from input. 'full': both internal cleavage sites must match. 'semi': one of two internal cleavage sites must match. 'none': allow all peptide hits no matter their context (enzyme is irrelevant).

Views

MSFraggerAdapter Std Output

The text sent to standard out during the execution of MSFraggerAdapter.

MSFraggerAdapter Error Output

The text sent to standard error during the execution of MSFraggerAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

• No workflows found

Links

• No links available

Developers