PEAKS - Version Online 12 -High-Throughput, All-in-One Software for Proteomics LC-MS/MS Analysis

Distributed System for High performance Computing

PEAKS Online uses the latest distributed computing technology to achieve high-throughput performance with established PEAKS workflows for multiple users on a network. The Master is at the centre of the system, it accepts computing request from a client or directly from the MS instrument using an automated system; PEAKS daemon: Automated Instrument Link. The Master will distribute all the computing workload to different workers, where the computation is performed. Use the Command Line Interface (CLI) to automate standard workflows and enable batch submission for large-cohort studies. All the data which is necessary for computation will be stored in the distributed database system. Since both computation and data storage are distributed to many different nodes, single node failure will not block the whole system. Therefore, the system is always accessible to the users. Additionally, because of the distribution, the system is also highly scalable, with the ability to add additional nodes at anytime to achieve maximum performance.

Enhanced DIA Workflow: Library Search, Direct Database Search, de novo sequencing

DIA analysis is an appealing alternative to DDA approach for an increased proteins coverage. In the past, DIA methods have relied on generating spectral libraries from DDA to identify and quantify peptides.

PEAKS Online 12 offers a unique streamlined DIA workflow to maximise identification of peptides by integrating three methods: spectral library search, direct database search, and de novo sequencing, with up to 20% increase in identification and quantification.

Selecting library search followed by the direct database search results in improved protein identification rates while the completeness of proteome is further enhanced by de novo sequencing. Beside in-depth identification analysis, PEAKS Online allows for quantification of DIA data by LFQ. Finally, an optional QC (Quality Control) will provide identification-related and quantification-related quality control measures to ensure experimental consistency, data quality and identification and quantification consistency.

Quality Control (QC) Function for in-depth analysis from raw data to results

PEAKS Online is designed to facilitate accurate and sensitive proteomic analysis using the PEAKS 12 software workflows, but with higher performance on a shared resource. Users will be able to perform de novo Sequencing, PEAKS DB Database Search, PEAKS Library Search, PEAKS PTM, and SPIDER, as in PEAKS Studio package. Optional PEAKS Q, and PEAKS IMS modules can be enabled, for labelled and label free protein quantification and ion mobility data support.

PEAKS Online provides users with the ability to utilise the established PEAKS workflows more efficiently and on a larger scale. The interactive tool used to send/retrieve data to/from the server is called PEAKS Client, and the results are presented in a similar manner as available in the PEAKS Studio desktop solution. Through the Web Client Interface or Client Command Line Interface (CLI), multiple users can also access the PEAKS Online server at the same time, supporting parallelism at the project and data level.

Smart data processing, is efficient data processing. If an analysis needs to be rerun with a new set of parameters, the whole workflow does not need to be reprocessed. This is perfect for certain applications like Time Course Studies and samples can be added to an existing project and workflows can be modified “on the fly”. PEAKS Online will only process the data that needs to be updated while keeping any of the relevant information generated previously. Once the desired results have been generated, users can export the results for each individual sample, or export all the results at once in a single step.

PEAKS DIA Workflows

• Up to 20% increase in peptide/protein identification and quantification
• Hybrid-DIA for targeted and discovery-driven clinical proteomics (PEAKS Studio Only)

DeepNovo Peptidome workflow

• Gene table to bridge the gap between proteomics and genomics
• Support for non-canonical reference sequences
• Label-free quantification and automated QC tool
• DeepNovo-DIA peptidome workflow

DeepNovo Workflow

• Upgraded DeepNovo function with GraphNovo algorithms [1]
• GPU-enabled for increased speed
• New FDR Estimation for de novo sequencing

PRM Workflow

• New PRM Targeted Quantification (PEAKS Studio Only)
• Transition list export: from DIA LFQ results, users can export PRM and MRM transition lists

Label-free quantification

• Feature Based LFQ: LFQ result with feature vectors with and without identification.
• Label-free Quantification Principal Component Analysis (PCA) plot added to all LFQ results
• Volcano plot improvements

Post-translational modification (PTM) and Mutations analysis

• Next level confidence: confident PTM/mutation sites identification based on amino acid level evidence

User experience, automation, and more

• Batch submission option
• Database validation
• Data Refine feature filter
• Automatic export option
• Image export in SVG format (PEAKS Studio Only)
• PSM ion export