The new PEAKS 6 user-friendly interface incorporates several different views of the results that can allow users to view their results on a protein, peptide, and even amino acid level. The following images briefly explain and illustrate the different views in PEAKS 6.
In the protein view, users are able to see everything going on at the protein level. Each identified protein is listed in the top pane along with associated results for each identification. By simply clicking on a protein, users can take a closer look at the protein coverage view. In this view, users can visualize the protein sequence, and clearly see what PTMs and mutations were confidently identified in the spectra.
The peptide view gives an in-depth look into what is going on aat the peptide level. Users can take a closer look at what peptides were identified and the associated statistics. Users are also able to differentiate which algorithm was used to identify the associated peptide, whether PEAKS DB, de novo sequencing, PEAKS PTM, or SPIDER.
Summary View - Results Statistics
In the Summary View section, users are able to validate and visualize the results. Easily select an FDR percentage, or de novo local confidence percentage from this view. The results statistics section gives users an excellent birds eye view of what has been identified in the study as well as an overview of the precursor mass errors detected. Users are also able to easily export the results in several popular formats.
Summary View - Experimental Control
Additionally, the summary view contains a section that is used to validate the experimental control in the study. In this view, users are able to take a closer look at the accuracy of their instrument.
De Novo Only View
The de novo only view allows users to take a closer look at all peptides that were confidently identified using our de novo sequencing algorithm but were not identified by our database search. These identifications represent potentially novel peptides that have not been sequenced yet.
Multi-Engine Summary View
In our multi-engine inChorus tool, users are able to run their data using multiple engines such as PEAKS, Mascot, Sequest, OMSSA, and XTandem! In the inChorus summary view users are able to get a bird's eye view of the overall identifications of each engine, as well as a Venn diagram illustrating overlapping identifications. InChorus allows users to set an FDR for each specific engine, or, users can set an overall FDR.
Multi-Engine - Peptide View
Another great function integrated in the inChorus tool, is the ability to see which engines identify specific peptides. Users can see which peptides were missed by specific engines and which peptides were confidently identified by all engines.