- 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-based: TMT (MS2, MS3) / iTRAQ, SILAC, 18O labeling, ICAT
- Supporting fragmentation types
- CID, HCD, ETD/ECD, EThcD, IRMPD, and UVPD
Complete Solutions for Bottom-up Discovery Proteomics
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.
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.
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.
The PEAKS Studio license can be scaled to address your lab’s requirements.
- Desktop – 8 threads, capable of processing across up to 8 cores
- Workstation – 16 threads, up to and across 16 cores
- MS Windows 32 or 64 bit
- Intel dual core processor
- 8GB RAM
- More than 1GB of free disk space to install
- MS Windows 64 bit
- Intel Core i7/Xeon Processor
- 16GB RAM or 2GB per core
- Tran NH, Zhang X, Xin L, Shan B, Li M. De novo peptide sequencing by deep learning. Proceedings of the National Academy of Sciences of the United States of America. 114(29). 18/7/2017.
- Tran NH, Rahman MZ, He L, Xin L, Shan B, Li M. Complete De Novo Assembly of Monoclonal Antibody Sequences Scientific Reports. 6(31730). 26/08/2016.
- Zhang J, Xin L, Shan B, Chen W, Xie M, Yuen D, Zhang W, Zhang Z, Lajoie GA, Ma B. PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification. Molecular & Cellular Proteomics. 11(4):1-8. 1/2/2012.