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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:
stty: 'standard input': Inappropriate ioctl for device
DecoyDatabase -- Creates combined target+decoy sequence database from forward sequence database.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_DecoyDatabase.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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 description 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 + decoy 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 appended (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 sequences 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 applicable if parameter 'type' is 'protein'. (default: 'Trypsin') (valid: 'Lys-C', 'Lys-N', 'Trypsin', 'Chymotrypsin', 'Chymotrypsin/P', 'CNBr', 'Formic_acid', 'PepsinA + P', 'cyanogen-bromide', 'Clostripain/P', 'Arg-C', 'Arg-C/P', 'Lys-C/P', 'PepsinA', 'Asp-N', 'Asp-N/B', 'Asp-N_ambic', 'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'leukocyte elastase', 'proline endopeptidase', 'glutamyl endopeptidase', 'Alpha-lytic protease', '2-iodobenzoate', 'iodosobenzoate', 'staphylococcal protease/D', 'proline-endopeptidase/HKR', 'Glu-C+P', 'elastase-trypsin-chymotrypsin', 'no cleavage', 'unspecific cleavage')
Parameters for neighbor peptide search ('in' holds the neighbor candidates):
-NeighborSearch:in_relevant_proteins <file> These are the relevant proteins, for which we seek neighbors (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 downstream filtering of search results via IDFilter and subsequent FDR.
-NeighborSearch:missed_cleavages <int> Number of missed cleavages for relevant and neighbor peptides. (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-res 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 peptide. (default: '0.01')
-NeighborSearch:pc_mass_tolerance_unit <choice> Is 'pc_mass_tolerance' in Da or ppm? (default: 'Da') (valid: '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. (default: '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