Pipeline Parameters

The LabKey Server data pipeline adds a set of parameters specific to the web site. These parameters are defined on the pipeline group. Most of these are set in the tandem.xml by the Search MS2 Data form, and will be overwritten if specified separately in the XML section of this form.

ParameterDescription

pipeline, database

The path to the FASTA sequence file to search. Sequence Database field.
pipeline, protocol nameThe name of the search protocol defined for a data file or set of files. Protocol Name field.
pipeline, protocol descriptionThe description for the search protocol. Protocol Description field.

pipeline, email address

Email address to notify of successful completion, or of processing errors. Automatically set to the email of the user submitting the form.

pipeline, load folderThe project folder in the web site with which the search is to be associated. Automatically set to the folder from which the search form is submitted.
pipeline, load spectraPrevents LabKey Server from loading spectra data into the database. Using this parameter can significantly improve MS2 run load time. If the mzXML file is still available, LabKey Server will load the spectra directly from the file when viewing peptide details. For example:
  • <note label="pipeline, load spectra" type="input">no</note>
Values are yes and no.
pipeline, data type

Flag for determining how spectrum files are searched, processed and imported.  The allowed (case insensitive) values are:

  • samples - Each spectrum data file is processed separately and imported as a MS2 Run into LabKey Server. (default)
  • fractions - Spectrum files are searched separately, then combined for further processing and imported together as a single MS2 Run into LabKey Server. Often used for MudPIT-style data.
  • both - All processing for both samples and fractions, both a MS2 Run per spectrum file as well as a combined MS2 Run are created

PeptideProphet and ProteinProphet Parameters

The LabKey data pipeline supports a set of parameters for controlling the PeptideProphet and ProteinProphet tools run after the peptide search. These parameters are defined on the pipeline prophet group.

ParameterDescription

pipeline prophet, min probability

The minimum PeptideProphet probability to include in the pepXML file (default - 0.05). For example:

  • <note type="input" label="pipeline prophet, min probability">0.7</note>
pipeline prophet, min protein probability

The minimum ProteinProphet probability to include in the protXML file (default - 0.05). For example:

  • <note type="input" label="pipeline prophet, min protein probability">0.7</note>
pipeline prophet, decoy tagThe tag used to detect decoy hits with a computed probability based on the model learned. Passed to xinteract as the 'd' argument
pipeline prophet, use hydrophobicityIf set to "yes", use hydrophobicity / retention time information in PeptideProphet. Passed to xinteract as the 'R' argument
pipeline prophet, use pI

If set to "yes", use pI information in PeptideProphet. Passed to xinteract as the 'I'argument

pipeline prophet, accurate massIf set to "yes", use accurate mass binning in PeptideProphet. Passed to xinteract as the 'A' argument
pipeline prophet, allow multiple instrumentsIf set to "yes", emit a warning instead of exit with error if instrument types between runs is different. Passed to xinteract as the 'w' argument
pipeline prophet, peptide extra iterationsIf set, the number of extra PeptideProphet iterations. Defaults to 20.
pipeline, import prophet resultsIf set to "false", do not import PeptideProphet or ProteinProphet results after the search. Defaults to "true".

Pipeline Quantitation Parameters

The LabKey data pipeline supports a set of parameters for running quantitation analysis tools following the peptide search. These parameters are defined on the pipeline quantitation group:

ParameterDescription

pipeline quantitation, algorithm

This parameter must be set to run quantitation. Supported algorithms are xpress, q3, and libra.

pipeline quantitation, residue label mass

The format is the same as X! Tandem's residue, modification mass. There is no default value. For example:

  • <note label="pipeline quantitation, residue label mass" type="input">9.0@C</note>
pipeline quantitation, mass toleranceThe default value is 1.0 daltons.
pipeline quantitation, mass tolerance unitsThe default value is "Daltons"; other options are not yet implemented.
pipeline quantitation, fixPossible values "heavy" or "light".
pipeline quantitation, fix elution referencePossible values "start" or "peak". The default value is "start".
pipeline quantitation, fix elution differenceA positive or negative number.
pipeline quantitation, metabolic search typePossible values are "normal" or "heavy".
pipeline quantitation, q3 compatIf the value is "yes", passes the --compat argument when running Q3. Defaults to "no".
pipeline quantitation, libra config nameName of Libra configuration file. LabKey Server supports up to 8 channels. Must be available on server's file system in <File Root>/.labkey/protocols/libra. Example file.
pipeline quantitation, libra normalization channelLibra normalization channel. Should be a number (integer) from 1-8.

ProteoWizard msconvert Parameters

LabKey Server can be configured to use ProteoWizard's msconvert tool to convert from instrument vendor binary file formats to mzXML. As of version 12.1, the Windows installer configures the server to automatically use msconvert for converting Thermo .RAW files to .mzXML, and 15.3 adds support for SciEx .wiff files.

ParameterDescription

pipeline msconvert, conversion bits

Number of bits of precision to use when converting spectra to mzXML. Possible values are "32" or "64". Defaults to not specifying a bit depth, leaving it to the msconvert default (64).

pipeline msconvert, mz conversion bits

Number of bits of precision to use for encoding m/z values. Possible values are "32" or "64". Defaults to not specifying a bit depth, leaving it to the msconvert default (64). (Added in 15.3)
pipeline msconvert, intensity conversion bitsNumber of bits of precision to use for encoding intensity values. Possible values are "32" or "64". Defaults to not specifying a bit depth, leaving it to the msconvert default (32). (Added in 15.3)
pipeline msconvert, indexPass-through parameters to control --filter arguments to msconvert. (Added in 15.3)
pipeline msconvert, precursorRecalculation
pipeline msconvert, precursorRefine
pipeline msconvert, peakPicking
pipeline msconvert, scanNumber
pipeline msconvert, scanEvent
pipeline msconvert, scanTime
pipeline msconvert, sortByScanTime
pipeline msconvert, stripIT
pipeline msconvert, msLevel
pipeline msconvert, metadataFixer
pipeline msconvert, titleMaker
pipeline msconvert, threshold
pipeline msconvert, mzWindow
pipeline msconvert, mzPrecursors
pipeline msconvert, defaultArrayLength
pipeline msconvert, chargeStatePredictor
pipeline msconvert, activation
pipeline msconvert, analyzerType
pipeline msconvert, analyzer
pipeline msconvert, polarity
pipeline msconvert, zeroSamples

 

ProteoWizard mspicture Parameters

LabKey Server can be configured to use ProteoWizard's mspicture tool to generate images from MS data files.

ParameterDescription

pipeline mspicture, enable

Calls mspicture as part of the workflow and associates the resulting images with the rest of the run. For example:
  • <note label="pipeline mspicture, enable" type="input">true</note>

MS2 Search Engine Parameters

For information on settings specific to particular search engines, see:

 

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