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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.


Additional Improvements

  • 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