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