Both DDA and DIA technologies are rapidly advancing, and researchers need an analysis method that combines the benefits of both acquisition methods. (Write something about DDA data) In recent years, DIA has become increasingly popular due to its parallel nature of acquiring all fragment ions for all precursors within a selected m/z range. This overcomes the limitations of sequential MS/MS acquisition in DDA.

Note: This option is currently only available in PEAKS Studio

DIA Analysis: Direct Database Search

PEAKS X’s new feature-based identification approach enables full DIA analysis support without the need of a spectral library. Acquired signals from DIA scans are analyzed directly to determine the peptide sequence and allow researchers to discover beyond the spectral library. To overcome the boundaries of discovery, we have introduced the first de novo sequencing algorithm for DIA data. With the combined de-novo and feature-based technique, we set to remove biases found in other available software packages.

Note: This option is currently only available in PEAKS Studio

PEAKS is well-known for its superior result visualization. Users have access to several different views of their results that allow viewing on a protein, peptide, and even amino acid level. PEAKS’ protein coverage view allows users to find a peptide of interest as well as pull up the associated spectra. Workflows allows even a beginner of PEAKS to easily analyze the data, while the built-in result validation guards the result quality and provides additional confidence. PEAKS graphical user interface is designed for easy interpretation, visualization and validation to help researchers reach the overall goal of their projects.

PEAKS offers a unique approach to its database search workflow by combining the derived de novo sequence with the corresponding database spectrum match. De novo peptide sequences are aligned with protein database entries to provide additional information about PTMs, mutations, homologous peptides, and novel peptides. PEAKS DB uses a tag-based search algorithm, which enables search accuracy and sensitivity. With PEAKS DB, researchers can fully characterize their sample by analyzing peptides whether in the database or not. Learn more

PEAKS offers a unique approach to its database search workflow by combining the derived de novo sequence with the corresponding database spectrum match. De novo peptide sequences are aligned with protein database entries to provide additional information about PTMs, mutations, homologous peptides, and novel peptides. PEAKS DB uses a tag-based search algorithm, which enables search accuracy and sensitivity. With PEAKS DB, researchers can fully characterize their sample by analyzing peptides whether in the database or not. Learn more

The identification of PTMs is achieved by integrating PEAKS DB and de novo sequencing results. The advanced algorithm included in PEAKS maximizes PTM identification and PTM profiling. PTM identification can be performed in PEAKS database searching and PEAKS PTM searching. In database searching, only a limited number of frequent known PTMs can be specified as variable modifications. Users can expand the PTM analysis by selecting PEAKS PTM in the identification workflow. Specify the PTMs of interest or search all 313 naturally occurring biological modifications from the Unimod database in your PEAKS PTM search. PEAKS PTM is specifically designed to discover unexpected modifications by integrating the powerful de novo sequencing algorithm and database searching. Don’t let your computational resources limit you. With PEAKS, maximize ID efficiency and thoroughly characterize PTMs in a complex proteome. Learn More

To handle mutations, PEAKS software includes SPIDER, an algorithm specially designed to detect peptide mutations and perform cross-species homology search. The SPIDER algorithm tries to match the de novo sequence tags with the database proteins. When a significant similarity is found, the algorithm tries to use both de novo sequencing errors and homology peptide mutations to explain the differences. SPIDER aims to reconstruct a “real” sequence to minimize the sum of de novo errors between the real sequence and the de novo sequence, and homology peptide mutations between the real sequence and the database sequence. Find confident hits that do not exist in the database with PEAKS’ de novo-based homology search. Learn More

To understand the functions of individual proteins in complex biological systems, it is often necessary to measure changes in protein abundance. As an optional add-on module, PEAKS Q allows scientists to determine relative protein abundance changes across a set of samples simultaneously by labeled or label-free quantification using LC-MS/MS. Learn more

Note: This option is currently only available in PEAKS Studio and PEAKS Online

Ion Mobility Spectrometry – Mass Spectrometry (IMS-MS) provides a compelling analytical workflow for complex biological and chemical mixtures by adding an additional dimension of ion separation; a 4th-dimension. With IMS-MS, ions are separated based on their mobility through a buffer gas, which provides the capability to differentiate ions based on their size, shape, charge and mass mobilities. Thus, it is possible to resolve ions that may be indistinguishable by traditional mass spectrometry.

With PEAKS IMS, analyze IMS-MS data using any of the PEAKS workflows, including: de novo sequencing, PEAKS DB, spectral library search, PEAKS PTM, SPIDER and labeled/label-free quantification (requires PEAKS Q module). The additional dimension enables increased identification sensitivity with smaller sample amounts. Easy-to-use PEAKS graphical user interface categorizes the raw data into IM-MS, IM-MS/MS, and LC-IM/MS. Researchers can easily view 4-D feature detection and feature separation based on ion-mobility. Learn more

Note: This option is currently only available in PEAKS Studio and PEAKS Online