MascotAdapterOnline

Options

version

Version of the tool that generated this parameters file.

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)

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.

decoy

Set to true if mascot should generate the decoy database.

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.

batch_size

Number of spectra processed in one batch by Mascot (default 50000)

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.)

Workflows

• 02-download_and_analyze_raw_fileKNIME Hub
• Peptide Identification from MSKNIME Hub
• Protein label-free quantificationKNIME Hub
• Protein label-free quantificationKNIME Hub
• Search Engine CombinationKNIME Hub

Links

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Developers