PEAKS Studio 13’s DDA and DIA workflows have been completely upgraded, with a more streamlined process setup, a more user-friendly experience, and enhanced analysis algorithms, resulting in significantly improved software performance. PEAKS DIA’s analysis speed has increased several times over, and the new DIA SPIDER feature is far ahead of the competition, enabling the discovery of new peptide segments and sequence variant peptides not included in the database, thereby enabling deeper mining of DIA data. The newly added Feature view on the DIA results page makes DIA results more transparent and facilitates interactive spectrum verification.

New features:

PEAKS DIA proteomics

Significantly improved CPU and GPU computation speeds

Unprecedented high performance, improving sensitivity and accuracy

DIA sequence variation analysis enables deeper exploration

Feature view provides comprehensive result visualization

Optimized protein and peptide scoring enhances identification reliability

Protein quantification supports free selection between Top 3 and MaxLFQ methods

Free selection of whether to apply Precursor FDR/score thresholds for result filtering PEAKS DIA Peptidomics

Utilizes the powerful GraphNovo deep learning sequencing algorithm

DIA Peptidome workflow now includes sequence variation analysis

LFQ supports co-quantification of database-matched and sequence-variant peptides PEAKS DDA

Newly designed DDA proteomics and peptidomics workflows enhance usability and flexibility

PEAKS PTM and SPIDER identification results can be used for quantitative analysis

Added “Found by” filtering functionality in the peptide list Transition list automatic generation tool

The newly added “Transition List Generator” tool in the Tools list can directly generate transition lists for targeted proteomics analysis from PEAKS analysis results or based on fasta theoretical enzyme digestion. PRM quantitative analysis

The new version of PRM analysis supports SILAC labeling quantification to improve the accuracy of targeted quantification

Added timsTOF PRM quantitative analysis

PRM standard curve quantitative data is no longer required

Added PRM protein annotation to display protein matching results