 |
OpenMS
|
Peptide Identification with MSFragger
| pot. predecessor tools | → MSFraggerAdapter → | pot. successor tools |
|---|---|---|
| any signal-/preprocessing tool (in mzML format) | IDFilter or any protein/peptide processing tool |
MSFragger must be installed before this adapter can be used. This adapter is fully compatible with version 3.2 of MSFragger and later versions of MSFragger were tested up to version 3.5.
All MSFragger parameters (as specified in the fragger.params file) have been transcribed to parameters of this OpenMS util. It is not possible to provide an explicit fragger.params file to avoid redundancy with the ini file. This adapter creates an fragger.params file prior to calling MSFragger. If the fragger.params file should be inspected, set the -debug option to 2. MSFraggerAdapter will print the path to the working directory to standard out.
MSFragger can process multiple input files (mzML, mzXML) one after another. The number of output files specified must match the number of input spectra files. The output file is then matched to the input file by index. The default parameters of the adapter are the same as given by the official MSFragger manual.
Please cite: Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu & Alexey I Nesvizhskii MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics Nature Methods volume 14, pages 513–520 (2017) doi:10.1038/nmeth.4256
The command line parameters of this tool are:
MSFraggerAdapter -- Peptide Identification with MSFragger.
Important note:
The Regents of the University of Michigan ("Michigan") grants us permission to redistribute
the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available
for use on related service offerings supported by the University of Tubingen and the Center for
Integrative Bioinformatics.
Per the license agreement the use of the pipeline and associated materials is for academic
research, non-commercial or educational purposes. Any commercial use inquiries
...
Full documentation: http://www.openms.de/doxygen/release/3.2.0/html/TOPP_MSFraggerAdapter.html
Version: 3.2.0 Sep 18 2024, 16:00:56, Revision: e231942
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
To cite MSFraggerAdapter:
+ Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensiv
e peptide identification in mass spectrometry–based proteomics. Nature Methods volume 14, pages 513–52
0 (2017). doi:doi:10.1038/nmeth.4256.
Usage:
MSFraggerAdapter <options>
Options (mandatory options marked with '*'):
-license <license>* Set to yes, if you have read and
agreed to the MSFragger license
terms. (valid: 'yes', 'no')
-java_executable <file> The Java executable. Usually Java
is on the system PATH. If Java is
not found, use this parameter to
specify the full path to Java
-java_heapmemory <num> Maximum Java heap size (in MB)
(default: '3500')
-executable <path_to_executable>* Path to the MSFragger executable
to use; may be empty if the execut
able is globally available.
-in <file>* Input File with specta for MSFragg
er (valid formats: 'mzML', 'mzXML'
)
-out <file>* MSFragger output file (valid forma
ts: 'idXML')
-opt_out <file> MSFragger optional output file
(valid formats: 'pepXML')
-database <path_to_fasta>* Protein FASTA database file path
(valid formats: 'FASTA', 'fasta',
'fa', 'fas')
Search Tolerances:
-tolerance:precursor_mass_tolerance_lower <precursor_mass_tolerance> Lower precursor mass tolerance
(default: '20.0') (min: '0.0')
-tolerance:precursor_mass_tolerance_upper <precursor_mass_tolerance> Upper precursor mass tolerance
(default: '20.0') (min: '0.0')
-tolerance:precursor_mass_unit <precursor_mass_unit> Unit of precursor mass tolerance
(default: 'ppm') (valid: 'Da',
'ppm')
-tolerance:precursor_true_tolerance <precursor_true_tolerance> True precursor mass tolerance (win
dow is +/- this value). Used for
tie breaker of results (in spectra
lly ambiguous cases) and zero bin
boosting in open searches (0 disab
les these features). This option
is STRONGLY recommended for open
searches. (default: '0.0') (min:
'0.0')
-tolerance:precursor_true_unit <precursor_true_unit> Unit of precursor true tolerance
(default: 'ppm') (valid: 'Da',
'ppm')
-tolerance:fragment_mass_tolerance <fragment_mass_tolerance> Fragment mass tolerance (window
is +/- this value) (default: '20.0
') (min: '0.0')
-tolerance:fragment_mass_unit <fragment_mass_unit> Unit of fragment mass tolerance
(default: 'ppm') (valid: 'Da',
'ppm')
-tolerance:isotope_error <isotope_error> Isotope correction for MS/MS event
s triggered on isotopic peaks.
Should be set to 0 (disabled) for
open search or 0/1/2 for correctio
n of narrow window searches. Shift
s the precursor mass window to
multiples of this value multiplied
by the mass of C13-C12. (default:
'0') (valid: '0', '1', '2', '0/1/
2')
In-Silico Digestion Parameters:
-digest:search_enzyme_name <search_enzyme_name> Name of the enzyme to be written
to the pepXML file (default: 'Tryp
sin') (valid: 'Arg-C/P', 'Asp-N',
'Asp-N/B', 'Asp-N_ambic', 'Chymotr
ypsin', '2-iodobenzoate', 'iodosob
enzoate', 'staphylococcal protease
/D', 'Trypsin', 'Arg-C', 'Clostrip
ain/P', 'elastase-trypsin-chymotry
psin', 'no cleavage', 'unspecific
cleavage', 'Chymotrypsin/P', 'CNBr
...
mide')
-digest:search_enzyme_cutafter <search_enzyme_cutafter> Residues after which the enzyme
cuts (specified as a string of
amino acids) (default: 'KR')
-digest:search_enzyme_nocutbefore <search_enzyme_nocutbefore> Residues that the enzyme will not
cut before (default: 'P')
-digest:num_enzyme_termini <num_enzyme_termini> Number of enzyme termini (non-enzy
matic (0), semi (1), fully (2)
(default: 'fully') (valid: 'non-en
zymatic', 'semi', 'fully')
-digest:allowed_missed_cleavage <allowed_missed_cleavage> Allowed number of missed cleavages
(default: '2') (valid: '0', '1',
'2', '3', '4', '5')
-digest:min_length <digest_min_length> Minimum length of peptides to be
generated during in-silico digesti
on (default: '7') (min: '0')
-digest:max_length <digest_max_length> Maximum length of peptides to be
generated during in-silico digesti
on (default: '64') (min: '0')
-digest:mass_range_min <digest_mass_range_min> Min mass of peptides to be generat
ed (Da) (default: '500.0') (min:
'0.0')
-digest:mass_range_max <digest_mass_range_max> Max mass of peptides to be generat
ed (Da) (default: '5000.0') (min:
'0.0')
Variable Modification Parameters:
-varmod:clip_nterm_m Specifies the trimming of a protei
n N-terminal methionine as a varia
ble modification
-varmod:masses <varmod1_mass .. varmod7_mass> Masses for variable modifications
-varmod:syntaxes <varmod1_syntax .. varmod7_syntax> Syntax Strings for variable modifi
cations
-varmod:unimod <varmod1_unimod .. varmod7_unimod> Variable modifications in unimod
syntax, is added to mass+syntax
varmod list
-varmod:enable_common Enable common variable modificatio
ns (15.9949 M and 42.0106 [^)
-varmod:not_allow_multiple_variable_mods_on_residue Do not allow any one amino acid
to be modified by multiple variabl
e modifications
-varmod:max_variable_mods_per_peptide <max_variable_mods_per_peptide> Maximum total number of variable
modifications per peptide (default
: '2') (valid: '0', '1', '2', '3',
'4', '5')
-varmod:max_variable_mods_combinations <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 (default: '5000') (min:
'0' max: '65534')
Spectrum Processing Parameters:
-spectrum:minimum_peaks <minimum_peaks> Minimum number of peaks in experim
ental spectrum for matching (defau
lt: '10') (min: '0')
-spectrum:use_topn_peaks <use_topN_peaks> Pre-process experimental spectrum
to only use top N peaks (default:
'50') (min: '0')
-spectrum:minimum_ratio <minimum_ratio> Filters out all peaks in experimen
tal spectrum less intense than
this multiple of the base peak
intensity (default: '0.0') (min:
'0.0' max: '1.0')
-spectrum:clear_mz_range_min <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) (default: '0.0')
(min: '0.0')
-spectrum:clear_mz_range_max <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) (default: '0.0')
(min: '0.0')
-spectrum:max_fragment_charge <max_fragment_charge> Maximum charge state for theoretic
al fragments to match (default:
'2') (valid: '1', '2', '3', '4')
-spectrum:override_charge Ignores precursor charge and uses
charge state specified in precurso
r_charge range (parameters: spectr
um:precursor_charge_min and spectr
um:precursor_charge_max)
-spectrum:precursor_charge_min <precursor_charge_min> Min charge of precursor charge
range to consider. If specified,
also spectrum:override_charge must
be set) (default: '1') (min: '0')
-spectrum:precursor_charge_max <precursor_charge_max> Max charge of precursor charge
range to consider. If specified,
also spectrum:override_charge must
be set) (default: '4') (min: '0')
Open Search Features:
-search:track_zero_topn <track_zero_topn> Track top N unmodified peptide
results separately from main resul
ts internally for boosting feature
s. Should be set to a number great
er than search:output_report_topN
if zero bin boosting is desired
(default: '0') (min: '0')
-search:zero_bin_accept_expect <zero_bin_accept_expect> Ranks a zero-bin hit above all
non-zero-bin hit if it has expecta
tion less than this value (default
: '0.0') (min: '0.0')
-search:zero_bin_mult_expect <zero_bin_mult_expect> Multiplies expect value of PSMs
in the zero-bin during results
ordering (set to less than 1 for
boosting) (default: '1.0') (min:
'0.0')
-search:add_topn_complementary <add_topn_complementary> Inserts complementary ions corresp
onding 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 (default: '0') (min: '0')
-search:min_fragments_modeling <min_fragments_modeling> Minimum number of matched peaks
in PSM for inclusion in statistica
l modeling (default: '3') (min:
'0')
-search:min_matched_fragments <min_matched_fragments> Minimum number of matched peaks
for PSM to be reported. MSFragger
recommends a minimum of 4 for narr
ow window searching and 6 for open
searches (default: '4') (min:
'0')
-search:output_report_topn <output_report_topn> Reports top N PSMs per input spect
rum (default: '1') (min: '0')
-search:output_max_expect <output_max_expect> Suppresses reporting of PSM if
top hit has expectation greater
than this threshold (default: '50.
0') (min: '0.0')
-search:localize_delta_mass <localize_delta_mass> Include fragment ions mass-shifted
by unknown modifications (recomme
nded for open and mass offset sear
ches) (0 for OFF, 1 for ON) (defau
lt: '0') (min: '0')
Static Modification Parameters:
-statmod:add_cterm_peptide <add_cterm_peptide> Statically add mass in Da to C-ter
minal of peptide (default: '0.0')
(min: '0.0')
-statmod:add_nterm_peptide <add_nterm_peptide> Statically add mass in Da to N-ter
minal of peptide (default: '0.0')
(min: '0.0')
-statmod:add_cterm_protein <add_cterm_protein> Statically add mass in Da to C-ter
minal of protein (default: '0.0')
(min: '0.0')
-statmod:add_nterm_protein <add_nterm_protein> Statically add mass in Da to N-ter
minal of protein (default: '0.0')
(min: '0.0')
-statmod:unimod <fixedmod1_unimod .. fixedmod7_unimod> Fixed modifications in unimod synt
ax if specific mass is unknown,
e.g. Carbamidomethylation (C).
When multiple different masses
are given for one aminoacid this
parameter (unimod) will have prior
ity.
-reindex <choice> Recalculate peptide to protein
association using OpenMS. Annotate
s target-decoy information. (defau
lt: 'true') (valid: 'true', 'false
')
PeptideIndexing:
-PeptideIndexing:allow_nterm_protein_cleavage <choice> Allow the protein N-terminus amino
acid to clip. (default: 'true')
(valid: 'true', 'false')
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed
to be used by the TOPP tool (defa
ult: '1')
-write_ini <file> Writes the default configuration
file
--help Shows options
--helphelp Shows all options (including advan
ced)
INI file documentation of this tool:
1.9.1