PeptiLine

Data Transformation

Process peptidomic data, search for bioactive peptides, and export results.

1. Upload Data
2. Study Variables
3. Protein Mapping
4. Process & Export

Upload Peptidomic Data

Peptidomic Data File *
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CSV, TSV, or XLSX peptidomic results. Column names are auto-detected for Proteome Discoverer, MaxQuant, PEAKS, Spectronaut, and Skyline exports.
Download example file · Load example
OR
Drag & drop or click to select multiple files
Upload multiple Proteome Discoverer files to merge into a single dataset

Functional Annotation (Optional)

Upload a pre-computed functional annotation table, or search a functional database by sequence similarity.

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Pre-computed functional annotation results (columns: search_peptide, peptide, function) — skips the database search
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OR
Minimum sequence similarity for database matching
Upload your peptidomic data above first.

Define Study Variable Groups

Group your abundance columns into experimental conditions. If any columns are technical replicates, define them below first — they will be averaged into a single biological replicate and become available in the group selector.

Rename Abundance Columns (Optional)

Instrument exports often use long sample names (e.g. Abundance F1 Sample Threshold). Map them to shorter labels here first — the simplified names are used throughout the technical-replicate and grouping steps below.

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JSON file mapping new names to original column names, e.g. {"T_0.2a": "Abundance F1 Sample Threshold"}
Example JSON · Load example
Technical Replicate Assignment (Optional)
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JSON file mapping bio replicate names to lists of technical replicate columns, e.g. {"Sample_A": ["Sample_A ( rep1)", "Sample_A ( rep2)"]}
Example JSON
Available
Selected
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JSON file mapping group names to abundance columns, e.g. {"Control": ["T_0_2a", "T_0_2b"]}
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Available
Selected

Protein Mapping

Map Protein Identifiers

Resolve ambiguous protein mapping from search engines. Then, if your data has unknown protein names, you can provide your own FASTA file or fetch from UniProt.

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Additional FASTA protein sequences to supplement the default bovine/human milk protein database
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OR
Automatically look up any protein IDs in your data that aren't already in the database.
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Process Data

Merge all data, calculate group averages, and extract bioactive peptides.