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Troubleshooting

Getting Started

What differences do I need to know about between ProSightPC and ProSightPD?

ProSightPC is a standalone software supporting database creation, analysis of infusion data, and high-throughput LC/MS data. ProSightPD is a collection of nodes enabling top-down LC/MS data to be searched in the Proteome Discoverer application.

What is required for me to install ProSightPC or ProSightPD?

For ProSight PC:

  • Microsoft™ Windows™ 7 x64 Professional (English version) with current service pack
  • ProSight Lite (freeware from prosightlite.northwestern.edu)

For ProSight PD:

  • ProSightPC
  • Proteome Discoverer (x64 version)
  • Thermo Proteome Discoverer ThirdParty Components installer (also installs the ProSightPD nodes and ProSightPD with High Mass nodes)
  • Microsoft™ Windows™ 7 x64 Professional (English version) with current service pack
  • ProSight Lite (freeware from prosightlite.northwestern.edu)
How do I analyze my data with ProSightPC/PD?

RAW files can be read directly into either ProSightPC or ProSightPD (via Proteome Discoverer) for detailed descriptions of building and executing data analysis workflows in both software please refer to the Quick Start Guides which can be found below.

Where can I download databases?

Databases with PTMs and FASTA files (no PTMs) can be found here: proteinaceous.net/database-warehouse/

How do I search my infusion data in ProSightPC?

Click the Add Experiment icon, or choose Tools > Experiment Adder to open the Experiment Adder dialog box

In the Fragmentation Methods area, select the fragmentation method.

In the Precursor Ion Data/Type box, select the precursor mass type, either Manual or Upload. If you select Manual in the Precursor Ion Data/Type list, select the mass type of the precursor ion in the Mass Type box (either Monoisotopic or Average) and enter the precursor mass. If you select Upload in the Precursor Ion Data/Type list, enter the path and name of the ASCII text file or files containing the precursor ion data in the Text File box, or click Browse to browse for them.

(Optional) Select a predefined search in the box near the bottom of the dialog box.

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