Following are the common troubleshooting methods for the Proteome Discoverer tool.

Refer to the Proteome Discoverer documentation for details.

Proteome discoverer troubleshooting cases



There are two nearly identical text files for importing study information into Proteome Discoverer.

The AccelerOme instrument outputs two replicates for TMT and TMTpro based methods to maximize the total mass of labeled sample output. A corresponding injection is defined for each output replicate having a specific .raw file name. The two Proteome Discoverer study files contain the same study information but address the unique .raw file names expected from the time of LCMS data acquisition.

Once the LCMS .raw data for the AcclerOme system sample outputs is acquired, upon loading the study information and .raw data into Proteome Discoverer, the message, Create new study failed. Quan Method (method name like TMTpro 16 defined within AccelerOme input text file) is not available, is displayed.

This message can result when the quantitation method name defined in Proteome Discoverer does not match with the method defined in the AccelerOme system's study text file. Edit the .txt file to match with a quantitation method name that is defined in your Proteome Discoverer installation. For example, if you rename the Proteome Discoverer quantitation method to include your TMT batch information, you must change the name for this method in the AccelerOme system's study .txt file to be equal to the name as it is defined in Proteome Discoverer.

The AccelerOme files for LCMS data acquisition and analysis references C:\PATHTORAWDATA or a similar path.

Change the path in the .txt file, and/or within Xcalibur for sequence files to reflect an existing Windows directory on your Xcalibur data acquisition PC and/or your Proteome Discoverer data analysis PC.