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OMSSAAdapter

Annotates MS/MS spectra using OMSSA.

Web Documentation for OMSSAAdapter

Options

version: Version of the tool that generated this parameters file.
precursor_mass_tolerance: Precursor monoisotopic mass tolerance
precursor_error_units: Unit of precursor mass tolerance
fragment_mass_tolerance: Fragment mass error in Dalton
min_precursor_charge: Minimum precursor ion charge
max_precursor_charge: Maximum precursor ion charge
fixed_modifications: Fixed modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
variable_modifications: Variable modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
pc: The number of pseudocounts to add to each precursor mass bin
hs: the minimum number of m/z values a spectrum must have to be searched
tez: scaling of precursor mass tolerance with charge (0 = none, 1= linear)
tom: product ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact
tem: precursor ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact
tex: threshold in Da above which the mass of a neutron should be added in an exact mass search
zt: minimum precursor charge to start considering multiply charged products
z1: the fraction of peaks below the precursor used to determine if the spectrum is charge +1
zc: should charge +1 be determined algorithmically (1=yes)
zcc: how should precursor charges be determined? (1=believe the input file,2=use the specified range)
zoh: set the maximum product charge to search
v: number of missed cleavages allowed
enzyme: The enzyme used for peptide digestion.
no: minimum size of peptides for no-enzyme and semi-tryptic searches
nox: maximum size of peptides for no-enzyme and semi-tryptic searches
i: comma delimited list of id numbers of ions to search
sp: number of product ions to search
sb1: should first forward (e.g. b1) product ions be searched (1 = no, 0 = yes)
sct: should c terminus ions (e.g. y1) be searched (1 = no, 0 = yes)
x: comma delimited list of NCBI taxonomy ids to search (0 = all. This is the default)
hm: the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded
ht: number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide
hl: maximum number of hits retained for one spectrum. Note: even when set to 1 OMSSA may report multiple hits with different charge states
he: the maximum e-value allowed in the hit list. If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported.
mm: the maximum number of mass ladders to generate per database peptide
mnm: n-term methionine should not be cleaved
is: evalue threshold to include a sequence in the iterative search, 0 = all
ir: evalue threshold to replace a hit, 0 = only if better
ii: evalue threshold to iteratively search a spectrum again, 0 = always
chunk_size: Number of spectra to submit in one chunk to OMSSA. Chunks with more than 30k spectra will likely cause memory allocation issues with 32bit OMSSA versions (which is usually the case on Windows). To disable chunking (i.e. submit all spectra in one big chunk), set it to '0'.
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)

Input Ports

: Input file [mzML]
: NCBI formatted FASTA files. The .psq filename should be given, e.g. 'SwissProt.fasta.psq'. If the filename does not end in '.psq' (e.g., SwissProt.fasta) the psq suffix will be added automatically. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' [psq,fasta]

Output Ports

: Output file [idXML]

Views

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

Workflows

Developers

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Plugin version: 2.7.0.202109131426

On NodePit since: 2022-12-06

Last update: 2024-11-09

KNIME versions: From v3.6 to v4.7

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