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OMSSAAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

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
Overwrite 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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

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