Application

The Application section explains how people move through LAMPrEY once the platform is running.

At a high level, the workflow is:

an administrator creates a project and pipeline
a user opens the configured pipeline
the user uploads one or more .raw files
LAMPrEY processes each run with MaxQuant and RawTools
the user reviews run outputs in Main and compares QC in Dashboard

Workflow overview

flowchart TD A["Admin panel: create project"] --> B["Admin panel: create pipeline"] B --> C["Main: open project"] C --> D["Main: open pipeline"] D --> E["Main: upload RAW files"] E --> F["LAMPrEY: run MaxQuant and RawTools"] F --> G["Main: inspect run details and outputs"] F --> H["Dashboard: compare QC across runs"]

How the Application section is organized

Admin panel

Use the Admin panel pages for one-time setup and configuration tasks:

create users
create projects
prepare and upload mqpar.xml
create pipelines

This is the setup layer that makes the rest of the application usable.

Main

Use Main for operational work:

browse projects
open pipelines
upload .raw files
monitor queue and run state
inspect individual run outputs

This is where most day-to-day submission and run tracking happens.

Dashboard

Use Dashboard after runs have completed:

review QC plots
compare metrics across runs
spot outliers and trends

This is the analysis layer for cross-run quality review.