Set up your analysis
Choose the input you have. Save everything under one project folder.
Choose where to save this analysis. Use a new folder, or load a saved project to continue it.
Choose an output folder to see where results will be written.
MaxQuant LFQ intensity columns and GN= gene annotations are recognized. Cover pages and differential-result sheets are skipped.
The recorded design is reused. Completed outputs are verified; incomplete reporting is rebuilt from verified inputs.
Discover acquisitions, then drag their cards into conditions. You can also import a sample table containing raw_path.
Import sample_id and condition to prefill assignments, or leave this blank and discover samples from your matrix or raw folder. For raw tables, include raw_path.
Assign and name your samples
Drag detected samples into a condition, or use the dropdown on each card. Drag between columns to correct an assignment, or back to Unassigned to exclude a sample. Edit sample and condition names as needed.
Only assigned samples enter the matrices, benchmarks and comparisons. Conditions are never inferred from filenames. Source filenames and columns remain linked when you rename a sample.
Review your analysis
Every pair of conditions will be compared at protein and available gene levels.
Use independent samples for different patients. For matrix data measured across conditions in the same donors, select paired comparisons below. Matrix imports require one quantity per donor/condition. For BAF, give technical injections the same biological sample ID on their cards.
Import this column with your sample table, or enter donor IDs on the sample cards in step 1. Matching uses these IDs, never filenames.
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.
Saved assignments used by this analysis
Saved in config/sample_assignments.csv and .tsv, including excluded samples.
| Analysis sample | Condition | Source |
|---|
Progress
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