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Introduction

Welcome to the Proteomics_Data_Processor wiki!

The Proteomics Data Processor is a Windows-based application designed to integrate with MSConnect and automate the processing of mass spectrometry data using third party identification software, such as FragPipe, DIA-NN, and ProteomeDiscoverer. It provides users with real time feedback on the quality of MS analysis, such as the number of protein and peptide identification to aid decision making process. This tool works in tandem with MSConnect to process the MS-based proteomics data. The program is built on C# with .net 4.5.1 (same framework as Thermo Orbitrap Tribride) for Windows platform.

User manual can be downloaded as a PDF from the following link. MSconnect_UserManual_Lav_1213_clear.pdf

The Key Features of Proteomics Data Processor include:

• Seamless communication with MSConnect.
• Automation of data processing through desktop tools.
• Designed for Windows systems with .NET Framework 4.5.1.
• Command-line configuration for admins and user-friendly GUI for researchers.

High-level overview

The processing workflow connects MSConnect with third-party tools like FragPipe and DIANN for proteomics data analysis. Three components listed below are critical for the workflow :

• Wrappers: The tool installed to MSConnect server that bridges between MSConnect third-party applications, and processors/worker.
• Processors/worker: It is the Proteomics Data Processor that downloaded and installed to the computer and is used to execute workflows configured in MSConnect server.
• Processing Workflows: Define the structure and logic for MS file data processing using the processor/worker.

The Proteomics Data Processor can be installed on multiple PC to create more node for Parallel Processing. This section provides a comprehensive guide for setting up the processing workflow after the MSConnect server has been initialized. Note that the Proteomics Data Processor is also referred to as Processing application, or Processing worker.