PEAKS^® Online 13.5

Distributed System for High Performance Computing

PEAKS Online uses the latest distributed computing technology to achieve high-throughput performance with PEAKS workflows for multiple users on a network. The Master is at the centre of the system; it accepts computing requests from clients and distributes the computing workload to the workers, which perform data processing and computation.

High-Throughput and Scalable

PEAKS Online is a proteomics data analysis platform designed for large scale projects and multiple users to support parallelism at project and data level. Worker and database nodes can be easily added for vertical and horizontal scalability.

Dual Interfaces

In PEAKS Online, dual interfaces are available to ensure easy integration into any proteomics workflow. The Web Client Interface allows users to set up and submit projects visually, as well as review and validate their results. The Client CLI on the other hand can be integrated into existing pipelines to allow for fully automated data processing.

Web Client Interface

Access Administrative Tools
Setup, View and Share Projects
Monitor Ongoing Processes and Modify Priority
Accessible on any OS

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Easily setup and access PEAKS projects from any computer, anywhere in the world. With PEAKS Online, users do not need to install any software files to access the server. Just open a web browser, like Google Chrome or Microsoft Edge, to set up PEAKS searches and review the results. When your search task is done, the system will even send you an email to let you know the search is complete.

Client CLI

Automated Batch Data Processing
Define Standardised Workflows
Easily Integrate into Existing Pipelines
Reduce Manual Intervention

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The command line interface gives users the ability to fully automate their data analysis. Simply establish standardised workflows so that once data is created in the repository, PEAKS Online will process and generate results instantaneously. Results generated using the Client CLI can be automatically exported into .csv files or viewed using the PEAKS Online Web Client.

Proteome and Peptidome Driven Workflows

In PEAKS Online the DDA and DIA workflows have been streamlined into two options: Proteome and Peptidome. Users can customise their analysis workflows selecting which step to run or modify. Results are organised into intuitive results nodes, making it easier to interpret, explore and validate your data.

DDA

DIA

Automated Large-Cohort Analyses

Introducing a new project type designed for rapid quality assessment and real-time overview of acquired data. This workflow uses automation of data uploading via instrument daemon, which continuously monitors the data repository for new files and uploads them to the server for analysis. Samples are processed in real time and exported to a predefined location.  Additionally, a cohort-level snapshot and summary statistics are dynamically updated throughout the analysis.

Real-time Quality Control

Exclusive to PEAKS Online, this pioneering workflow automatically screens QC samples, assesses technical variation across acquisition, and delivers a comprehensive interface for monitoring data processing status and flagging failed samples in real time. In the event a sample does not meet the defined QC criteria, an automated notification is dispatched to the user.

Custom Management

Align your teams' efforts with administrative controls to standardise workflows, databases, PTMs, and quantification methods across your entire team from a single interface. The Worker and Master Monitors provide clear, real-time visibility into active tasks and system communications keeping operations transparent and efficient. Custom sharing capabilities further extend collaboration, allowing users to share projects and configurations such as modifications, enzymes and databases with other users. Easily control administrator and user accounts using the user management page with multi-user access to the PEAKS Online server at the same time.

PEAKS DeepNovo Peptidome

The DeepNovo Peptidome workflow is designed to bridge the gap between proteomics and genomics through the integration of a comprehensive gene table. The DDA workflow supports non-canonical reference sequences allowing for the identification of variant and modified sequences that are often missed by standard canonical reference databases. DIA Peptidome now has support for spectral library and target peptide list to search for target peptides expected to be found in the sample.

DDA Peptidome

DIA Peptidome

Enhanced DIA Proteome Workflow

PEAKS offers a robust solution for DIA data analysis. First, an optional library search is performed against a library of previously identified spectra. By estimating the false discovery rate, peptides that pass the filter are saved. MS/MS spectra that don’t match a peptide within the false discovery rate threshold are brought forward to a direct database search. Confident database matches are added to the result. Next, unmatched spectra from the database search are analysed using de novo sequencing. Those peptides passing the average local confidence score will further be subjected to SPIDER algorithm.

Sequence Variants

Dive beyond traditional proteomics in PEAKS Online. Uncover sequence variants using SPIDER and Novel Peptides with de novo sequencing.

Quantification

With PEAKS Q module it enables labs to uncover changes in protein expression. Quantify peptide/protein abundances across samples using label-free or labelled quantification techniques. Intuitive result views allow you to assess the quality of the sensitive and reproducible results through heat maps, volcano plots, and extracted ion chromatograms.