Key Features:

• Peptide/Protein identification
  • de novo sequencing
  • Database search
  • Post-translational modification (PTM) search with 500+ modification
  • Sequence variant and mutation search
• Protein quantification in complex biological samples
  • Label-free
  • Label-based: TMT (MS2, MS3) / iTRAQ, SILAC, 18O labeling, ICAT, User-Defined
• Supporting fragmentation types
  CID, HCD, ETD/ECD, EThcD, IRMPD, and UVPD
• Supporting DDA, DIA, and ion mobility data analysis

PEAKS X is peptide feature-based. Feature table lists all peptide features detected from LC-MS, along with their peptide identifications by database search or de novo sequencing. Each feature is linked to protein view, spectrum view and LC-MS view for inspection.

PEAKS Studio performs LC-MS/MS data analysis and statistics according to the experimental design. Following the identification of peptides with MS/MS spectra, the resulting peptide sequences are used to determine the original protein components of the samples.

The Protein View presents protein profiling across complex biological samples. For each protein, the Sequence Coverage View displays a peptide map with spectrum annotation for validation. For more information about proteomics database searching, visit the PEAKS DB page.

The Peptide View provides a list of identified peptides with the abundance from MS1. For each modified peptide, the confidence of modification site (Ascore) is associated. For more information about modified peptides and PTM analysis, visit the PEAKS PTM page.

With the add-on module of PEAKS Q, PEAKS Studio also determines relative protein abundance changes across a set of samples simultaneously and without the requirement for prior knowledge of the proteins involved.

Highly differentially expressed proteins between two groups are identified by statistical analysis tool (fold change >2, FDR < 0.01) and displayed in a heatmap format.