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MascotAdapterOnline

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Annotates MS/MS spectra using Mascot.

Web Documentation for MascotAdapterOnline

Options

version
Version of the tool that generated this parameters file.
keep_protein_links
The Mascot response file usually returns incomplete/wrong protein hits, so re-indexing the peptide hits is required. To avoid confusion why there are so few protein hits and force re-indexing, no proteins should be reported. To see the original (wrong) list, enable this flag.
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)
database
Name of the sequence database
search_type
Name of the search type for the query
enzyme
The enzyme descriptor to the enzyme used for digestion. (Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server).
instrument
Instrument definition which specifies the fragmentation rules
missed_cleavages
Number of missed cleavages allowed for the enzyme
precursor_mass_tolerance
Tolerance of the precursor peaks
precursor_error_units
Units of the precursor mass tolerance
fragment_mass_tolerance
Tolerance of the peaks in the fragment spectrum
fragment_error_units
Units of the fragment peaks tolerance
charges
Charge states to consider, given as a comma separated list of integers (only used for spectra without precursor charge information)
taxonomy
Taxonomy specification of the sequences
fixed_modifications
List of fixed modifications, according to UniMod definitions.
variable_modifications
Variable modifications given as UniMod definitions.
special_modifications
Modifications with specificity groups that are used by Mascot and have to be treated specially
mass_type
Defines the mass type, either monoisotopic or average
number_of_hits
Number of hits which should be returned, if 0 AUTO mode is enabled.
skip_spectrum_charges
Sometimes precursor charges are given for each spectrum but are wrong, setting this to 'true' does not write any charge information to the spectrum, the general charge information is however kept.
search_title
Sets the title of the search.
username
Sets the username which is mentioned in the results file.
email
Sets the email which is mentioned in the results file. Note: Some server require that a proper email is provided.
hostname
Address of the host where Mascot listens, e.g. 'mascot-server' or '127.0.0.1'
host_port
Port where the Mascot server listens, 80 should be a good guess
server_path
Path on the server where Mascot server listens, 'mascot' should be a good guess
timeout
Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps. Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!
boundary
Boundary for the MIME section
use_proxy
Flag which enables the proxy usage for the HTTP requests, please specify at least 'proxy_host' and 'proxy_port'
proxy_host
Host where the proxy server runs on
proxy_port
Port where the proxy server listens
proxy_username
Login name for the proxy server, if needed
proxy_password
Login password for the proxy server, if needed
login
Flag which should be set 'true' if Mascot security is enabled; also set 'username' and 'password' then.
username
Name of the user if login is used (Mascot security must be enabled!)
password
Password of the user if login is used (Mascot security must be enabled!)
use_ssl
Flag indicating whether you want to send requests to an HTTPS server or not (HTTP). Requires OpenSSL to be installed (see openssl.org)
export_params
Adjustable export parameters (passed to Mascot's 'export_dat_2.pl' script). Generally only parameters that control which hits to export are safe to adjust/add. Many settings that govern what types of information to include are required by OpenMS and cannot be changed. Note that setting 'query_master' to 1 may lead to incorrect protein references for peptides.
skip_export
For use with an external Mascot Percolator (via GenericWrapper): Run the Mascot search, but do not export the results. The output file produced by MascotAdapterOnline will contain only the Mascot search number.

Input Ports

input file in mzML format.#br# [mzML]

Output Ports

output file in idXML format.#br# [idXML]

Views

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

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Update Site

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

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