PEAKS Studio

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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
  • Supporting fragmentation types

Complete Solutions for Bottom-up Discovery Proteomics

PEAKS Protein Identification & Quantification Softtware

Proteomics is the study of proteins expressed in a given type of cell, tissue or organism under particular biological conditions at a given time. Shotgun (or bottom-up) proteomics is the most commonly used MS-based approach to study proteins by digesting proteins into peptides prior to MS analysis. PEAKS Studio is a software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post-translational modifications (PTMs) and sequence variants (mutations), and peptide/protein de novo sequencing.

Software Overview

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.

Protein View

PEAKS - Protein Identification View

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.

Peptide View

PEAKS - Peptide Identification View

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.

Quantification View

PEAKS Studio - Protein Quantification View


a. Integrating de novo and database search to maximize peptide identification

De novo sequence tags were used:

  • to improve database search sensitivity and accuracy
  • to enhance modification search with +500
  • to find sequence variants with homology search
  • to infer new ORFs from novel peptides


Learn more about the advantages de novo sequencing brings to your research.

PEAKS Protein Identification Workflow

b. Intensity-based quantification with alignment to minimize missing-value variance

PEAKS Studio - LC-MS/MS Discovery Proteomics Software