Wednesday, October 16, 2013

PEAKS 7 Beta Starts Today

The PEAKS team was extremely busy in the past several weeks and finally today we are able to put PEAKS 7 beta in our invited testers' hands.

The biggest new feature in PEAKS 7 is the new label free quantification algorithm, which will replace the old algorithm in the optional quantification module. Our HUPO 2013 poster, PEAKS - A Software Tool for Shotgun Label Free Proteomics with High Sensitivity and High Accuracy, showed some preliminary results. To help our user navigating through the data and results for manual inspection, we have re-engineered the 2D heatmap and 3D view to provide a smooth, Google Map-like experience.

PEAKS is already the best commercial de novo sequencing solution. In PEAKS 7, we make it even better by tackling two fronts: improving accuracy and providing result validation/filtration. This poster shows that when the peptides are fragmented using different fragmentation methods the accuracy of de novo sequencing can be significantly improved. PEAKS 7 also includes tools and guidelines for de novo result filtering and validation, described in this poster.

There are many more improvements in PEAKS 7, we will unveil them at release, shall we?

We may expand our tester base slightly in the next few weeks depending on the stability of the beta build. If you are willing to get early access to PEAKS 7, please comment on the post or send email to Although we cannot guarantee your early access, we will make sure that you get notified as soon as PEAKS 7 released.

Wednesday, October 2, 2013

Local confidence score and de novo tags

PEAKS de novo sequencing not only produces accurate de novo sequences from the spectrum, it also provides confidence score at amino acid level.

In the de novo table, when you hover the mouse cursor on a de novo sequence, the following window will show up to display the local confidence score for each amino acid.

The sequence is color coded. Red represents a very high confidence (greater than 90%), purple represents a high confidence (80 to 90%), blue represents a medium confidence (60 to 80%), and black represents low confidence (less than 60%).

PEAKS also provide a slider to change the low confident amino acid to mass tag. We call the remaining consecutive high confident amino acids de novo tag.

Those de novo tags may then be used in BLAST.