Protocol: X!Tandem Analysis: /home/Demos/CPAS/demo/icat

Protocol: X!Tandem Analysis

icat

Standard Properties

Name	X!Tandem Analysis
Contact
Instrument
Software
Description	Use X!Tandem to search for peptides in one mzXml file
Max input data per instance
Max input material per instance
Output data per instance
Output material per instance

Custom Properties

Category

xtandem

Protocol Parameters

ApplicationLSIDTemplate	${RunLSIDBase}:MS2.XTandemAnalysis
ApplicationNameTemplate	XTandem analysis run

Protocol Details

Material Inputs

Name Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Sample Set Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart
No data to show.

Data Inputs

Name Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Data Class Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart
No data to show.

Material Outputs

Name Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Sample Set Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart
No data to show.

Data Outputs

Name Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Data Class Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart
No data to show.

Protocol Steps

Step	Name	Description
1	X!Tandem Analysis	Use X!Tandem to search for peptides in one mzXml file
50	XTandem analysis
60	Convert To PepXml
70	Run Peptide Prophet using XInteract
80	Run Protein Prophet using XInteract
1000	Mark Run Outputs

Runs Using This Protocol

Select All Select None Show Selected Show Unselected Show All	Flag Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart		Name Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Created Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Created By Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Protocol Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart	Run Groups Sort Ascending Sort Descending Clear Sort Filter... Clear Filter Remove Column Summary Statistics... Bar Chart Pie Chart Quick Chart
			CPAS/SmallICAT (ICATSrch)	2006-06-15 16:44	tamram	X!Tandem Analysis	Default Experiment