Set up your analysis
Choose the input you have. Save everything under one project folder.
Use a new folder for a new analysis. Load an existing project to review or continue it.
The recorded design is reused. Completed outputs are verified; incomplete reporting is rebuilt from verified inputs.
Scan this folder and assign conditions below, or provide a sample table containing raw_path.
| Sample ID | Condition | Acquisition |
|---|
CSV or TSV with sample_id and condition. For raw data, also include raw_path. A scanned sample list can replace this table.
Review your analysis
Every pair of conditions will be compared at protein and available gene levels.
This model assumes independent samples. For repeated patients, leave comparisons off and use a tailored statistical design.
GN= annotations supply missing gene symbols. DIA needs target-only FASTA; DDA needs a validated search FASTA with contaminants and matching rev_ decoys.
Reports shared proteins, pipeline-only proteins, service-only proteins, and the net difference per sample and overall.
Use the pinned versions listed in the installation guide. The advanced raw editor also prepares FASTA databases and supports DDA+.
The original run supplies its sample design, input files and statistical settings. Reuse checks happen before execution.
Advanced settings
An imported native configuration supplies its own sample design and comparison settings.
Run & find results
Save a project first.
New projectYou can close this page after launching. Reopen this project to follow progress. Stop preserves the project for continuation.
Progress
No analysis started.