What Are the New Features in the ProteinPilot™ Software Found in the OneOmics™ Suite 3.3?

For research use only. Not for use in diagnostic procedures.

Answer

ProteinPilot™ software 5.0.3 in the OneOmics™ suite 3.3 now offers almost the same features as the desktop version of ProteinPilot software. When opening the OneOmics suite is opened, there are several tiles that appear (see below). The tile for ProteinPilot software is located in the Identify section. 



Once the ProteinPilot tile is selected, users can start processing data in ProteinPilot software. Processing begins by entering the search parameters in the Create Workflow Wizard for ProteinPilot software. An example is shown below.



The new software features introduced in ProteinPilot software 5.0.3 are located under the following sections: Search Efforts, Special Factors, and Instrument. Even .mgf data files acquired on non-SCIEX instruments can be compared using the same search conditions in ProteinPilot software.

1) Under Search Effort/ID Focus, the option Thorough/Biological modifications can be selected as shown above. Now in the new version, users can also select the following options: Rapid/ None, Thorough/ Amino acid substitutions, or Thorough/ Biological modifications and Amino acid substitutions (see below) in addition to the options that were there in prior versions. 



2) The Special Factors menu provides a set of experimental options similar to those embedded in the 5.0.2 desktop version of ProteinPilot software. However, customizing these Special Factor options can still only be done in the desktop version of ProteinPilot software.


3) The Instrument section contains new options in the Instrument Choice menu. These new options allow for the use of the MGF file format from other vendors so that results can be compared with the same search parameters.