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.
| Parameter | Description |
|
pipeline, database |
The path to the FASTA sequence file to search. Sequence Database field. |
| pipeline, protocol name | The name of the search protocol defined for a data file or set of files. Protocol Name field. |
| pipeline, protocol description | The 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 folder | The 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 spectra | Prevents 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:
|
| pipeline, data type |
Flag for determining how spectrum files are searched, processed and imported. The allowed (case insensitive) values are:
|
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.
| Parameter | Description |
|
pipeline prophet, min probability |
The minimum PeptideProphet probability to include in the pepXML file (default - 0.05). For example:
|
| pipeline prophet, min protein probability |
The minimum ProteinProphet probability to include in the protXML file (default - 0.05). For example:
|
| pipeline prophet, decoy tag | The 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 hydrophobicity | If 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 mass | If set to "yes", use accurate mass binning in PeptideProphet. Passed to xinteract as the 'A' argument |
| pipeline prophet, allow multiple instruments | If 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 iterations | If set, the number of extra PeptideProphet iterations. Defaults to 20. |
| pipeline, import prophet results | If set to "false", do not import PeptideProphet or ProteinProphet results after the search. Defaults to "true". |
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:
| Parameter | Description |
|
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:
|
| pipeline quantitation, mass tolerance | The default value is 1.0 daltons. |
| pipeline quantitation, mass tolerance units | The default value is "Daltons"; other options are not yet implemented. |
| pipeline quantitation, fix | Possible values "heavy" or "light". |
| pipeline quantitation, fix elution reference | Possible values "start" or "peak". The default value is "start". |
| pipeline quantitation, fix elution difference | A positive or negative number. |
| pipeline quantitation, metabolic search type | Possible values are "normal" or "heavy". |
| pipeline quantitation, q3 compat | If the value is "yes", passes the --compat argument when running Q3. Defaults to "no". |
| pipeline quantitation, libra config name | Name 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 channel | Libra normalization channel. Should be a number (integer) from 1-8. |
LabKey Server can be configured to use ProteoWizard's msconvert tool to convert from instrument vendor binary file formats to mzXML.
| Parameter | Description |
|
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). |
| pipeline msconvert, intensity conversion bits | Number 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). |
| pipeline msconvert, index | Pass-through parameters to control --filter arguments to msconvert. |
| 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 |
LabKey Server can be configured to use ProteoWizard's mspicture tool to generate images from MS data files.
| Parameter | Description |
|
pipeline mspicture, enable |
Calls mspicture as part of the workflow and associates the resulting images with the rest of the run. For example:
|
For information on settings specific to particular search engines, see:
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