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PEAKS X – New Features
This page is dedicated to discussing new features available in PEAKS X. One of the most exciting new features is the feature-based identification method to its unique de novo assisted workflow to increase sensitivity and maximize peptide identification efficiency for in-depth shotgun analysis of complex proteomes. Other additions and changes include the following components:
Resolution for Chimeric Spectra
- Using the new MS1 feature-based identification approach, one MS2 scan can be associated with multiple peptide features within its acquisition window, enabling multiple peptide identifications per chimeric MS2 spectrum.
Spectral-Library-Free DIA Support
- PEAKS X’s new feature-based identification approach enables full DIA analysis support without the need of a spectral library. DIA spectra are analyzed directly to determine the peptide sequences of peptide features in their acquisition window, allowing peptide identifications beyond the information from a specific spectral library. With the combined de novo and feature-based technique, PEAKS removes biases found in commonly utilized approaches.
De Novo Sequencing for DIA Data
- PEAKS X introduces the first de novo sequencing solution for DIA data to provide non-biased results.
Improved Identification of Endogenous and Low Abundant Peptides
- PEAKS X improves analysis for endogenous peptide identifications by allowing variability at the C-terminus of peptides in no enzyme searching. This combined with feature-based peptide identification increases sensitivity when analyzing endogenous peptide datasets.
Ion-Mobility Spectrometry (IMS-MS) support
- IMS-MS data can be analyzed with PEAKS de novo, identification and quantification work flows and interactive data visualization tools allow data view projected on m/z-rt or m/z-1/k0 dimensions.
- Feature-based analysis for timsTOF data
- Support for Thermo Fisher Scientific’s Advanced Peak Determination (APD)
- Purity correction for TMT/iTRAQ
- Added TMT11-plex to built-in methods
- Added “Digest Mode” for sample analysis to support “No Digestion” samples
- Protein group FDR in identification result
- Added 1/k0 range in features table