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OpenMS
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Create a decoy peptide database from standard FASTA databases.
Decoy databases are useful to control false discovery rates and thus estimate score cutoffs for identified spectra.
The decoy can either be generated by reversing or shuffling each of the peptides of a sequence (as defined by a given enzyme). For reversing the N and C terminus of the peptides are kept in position by default.
To get a 'contaminants' database have a look at http://www.thegpm.org/crap/index.html or find/create your own contaminant database.
Multiple databases can be provided as input, which will internally be concatenated before being used for decoy generation. This allows you to specify your target database plus a contaminant file and obtain a concatenated target-decoy database using a single call, e.g., DecoyDatabase -in human.fasta crap.fasta -out human_TD.fasta
By default, a combined database is created where target and decoy sequences are written interleaved (i.e., target1, decoy1, target2, decoy2,...). If you need all targets before the decoys for some reason, use only_decoy and concatenate the files externally.
The tool will keep track of all protein identifiers and report duplicates.
Also the tool automatically checks for decoys already in the input files (based on most common pre-/suffixes) and terminates the program if decoys are found.
Extra functionality: The Neighbor Peptide functionality (see subsection 'NeighborSearch') is designed to find peptides (neighbors) in a given set of sequences (FASTA file) that are similar to a target peptide (aka relevant peptide) based on mass and spectral characteristics. This provides more power when searching complex samples, but only a subset of the peptides/proteins is of interest. See www.ncbi.nlm.nih.gov/pmc/articles/PMC8489664/ and NeighborSeq for details.
The command line parameters of this tool are:
DecoyDatabase -- Creates combined target+decoy sequence database from forward sequence database.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_DecoyDatabase.html
Version: 3.3.0-pre-nightly-2024-11-20 Nov 21 2024, 02:34:56, Revision: decb5c8
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.
Usage:
DecoyDatabase <options>
This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option
Options (mandatory options marked with '*'):
-in <file(s)>* Input FASTA file(s), each containing a database. It is
recommended to include a contaminant database as well.
(valid formats: 'fasta')
-out <file>* Output FASTA file where the decoy database (target + deco
y or only decoy, see 'only_decoy') will be written to.
(valid formats: 'fasta')
-decoy_string <string> String that is combined with the accession of the protein
identifier to indicate a decoy protein. (default: 'DECOY
_')
-decoy_string_position <choice> Should the 'decoy_string' be prepended (prefix) or append
ed (suffix) to the protein accession? (default: 'prefix')
(valid: 'prefix', 'suffix')
-only_decoy Write only decoy proteins to the output database instead
of a combined database.
-type <choice> Type of sequence. RNA sequences may contain modification
codes, which will be handled correctly if this is set to
'RNA'. (default: 'protein') (valid: 'protein', 'RNA')
-method <choice> Method by which decoy sequences are generated from target
sequences. Note that all sequences are shuffled using
the same random seed, ensuring that identical sequences
produce the same shuffled decoy sequences. Shuffled seque
nces that produce highly similar output sequences are
shuffled again (see shuffle_sequence_identity_threshold).
(default: 'reverse') (valid: 'reverse', 'shuffle')
-enzyme <enzyme> Enzyme used for the digestion of the sample. Only applica
ble if parameter 'type' is 'protein'. (default: 'Trypsin'
) (valid: 'Asp-N_ambic', 'Chymotrypsin', 'Chymotrypsin/P'
, 'CNBr', '2-iodobenzoate', 'iodosobenzoate', 'staphyloco
ccal protease/D', 'Trypsin', 'Arg-C', 'Arg-C/P', 'Asp-N',
'Asp-N/B', 'elastase-trypsin-chymotrypsin', 'no cleavage
', 'unspecific cleavage', 'Formic_acid', 'Lys-C', 'Lys-N'
, 'Lys-C/P', 'PepsinA', 'TrypChymo', 'Trypsin/P', 'V8-DE'
, 'V8-E', 'leukocyte elastase', 'proline endopeptidase',
'glutamyl endopeptidase', 'Alpha-lytic protease', 'prolin
e-endopeptidase/HKR', 'Glu-C+P', 'PepsinA + P', 'cyanogen
-bromide', 'Clostripain/P')
Parameters for neighbor peptide search ('in' holds the neighbor candidates):
-NeighborSearch:in_relevant_proteins <file> These are the relevant proteins, for which we seek neighb
ors (valid formats: 'fasta')
-NeighborSearch:out_neighbor <file> Output FASTA file with neighbors of relevant peptides
(given in 'in_relevant_proteins').
-NeighborSearch:out_relevant <file> Output FASTA file with target+decoy of relevant peptides
(given in 'in_relevant_proteins'). Required for downstrea
m filtering of search results via IDFilter and subsequent
FDR.
-NeighborSearch:missed_cleavages <int> Number of missed cleavages for relevant and neighbor pept
ides. (default: '0')
-NeighborSearch:mz_bin_size <num> Bin size for spectra m/z comparison (the original study
suggests 0.05 Th for high-res and 1.0005079 Th for low-re
s spectra). (default: '0.05')
-NeighborSearch:pc_mass_tolerance <double> Maximal precursor mass difference (in Da or ppm; see 'pc_
mass_tolerance_unit') between neighbor and relevant pepti
de. (default: '0.01')
-NeighborSearch:pc_mass_tolerance_unit <choice> Is 'pc_mass_tolerance' in Da or ppm? (default: 'Da') (val
id: 'Da', 'ppm')
-NeighborSearch:min_peptide_length <int> Minimum peptide length (relevant and neighbor peptides)
(default: '5')
-NeighborSearch:min_shared_ion_fraction <double> Minimal required overlap 't_i' of b/y ions shared between
neighbor candidate and a relevant peptide (t_i <= 2*B12/
(B1+B2)). Higher values result in fewer neighbors. (defau
lt: '0.25')
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 (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
The following configuration subsections are valid:
- Decoy Decoy parameters section
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
- http://www.openms.de/doxygen/nightly/html/TOPP_DecoyDatabase.html
INI file documentation of this tool:
1.9.1