This guide covers importing a peptide dataset from a HELM file (CSV/Excel) or an SDF, supplying a monomer library, and configuring peptide-specific options.
The Peptide dataset type is only available when the peptide plugin is enabled for your organization. If you do not see it, contact your administrator.
Step 1: Open the New Dataset wizard
From the Home page, click the Create Dataset card (or New → Create Dataset in the left navigation). The New Dataset wizard opens with three steps: Dataset Information, Properties Configuration, and Import Status.
Step 2: Choose the Peptide dataset type
Under Dataset Type, select Peptide.
Then choose the target Project and the Dataset File.
Accepted file formats for peptides:
| Format | Notes |
|---|---|
CSV / Excel (.csv, .csv.gz, .xlsx) |
Tabular files with a HELM column (required columns ID, Name, HELM; extra columns become properties). HELM references monomers by symbol only, so a monomer library is needed for any monomer not already in the Monomer Service. |
SDF (.sdf, .sd, .sdf.gz, .sd.gz) |
A V3000 SDF that carries the peptides and a monomer template for each monomer. The embedded templates are used to register any missing monomers on the Monomer Service, so no separate monomer library is needed. |
Use the Download peptide dataset templates links (CSV / Excel) in the dialog to start from a correctly formatted file. A minimal row looks like PEP001, Example Peptide, PEPTIDE1{A.G.K.L}$$$$.
Step 3: Supply a monomer library (CSV/Excel imports only)
A Monomer Library File maps each monomer symbol to its chemical structure so Ideation can register monomers that are not yet in the Monomer Service. It is needed only for CSV/Excel (HELM) imports — HELM references monomers by symbol without carrying their structures — and the picker appears only for those files.
The library maps each monomer symbol to its structure. At minimum it needs aSymbol and a CTAB (structure) column; Name, Short Name, and Natural Analog are optional. It can be a CSV, Excel, or SDF file.
For SDF dataset imports you do not provide a monomer library. A V3000 SDF already embeds a monomer template for every monomer, and those templates are used to register any missing monomers on the Monomer Service automatically — which is why the picker does not appear for SDF files.
Step 4: Configure peptide-specific options
Click Next. On the Properties Configuration step, a Peptide Specific Configuration section appears:
- HELM Column — the column that holds the HELM sequence notation (tabular imports only; auto-detected when named
HELM). - Reference Peptide — the peptide used by default as the basis for SAR slides created from this dataset. You can change it later per report.
Select and configure at least one main property, then submit.
Step 5: Watch the import
The final Import Status step shows the peptide import timeline:
Initializing → Registering Monomers → Parsing Peptide Sequences → Ready
The Registering Monomers stage runs when a monomer library was supplied, or when the dataset is a V3000 SDF (whose embedded monomer templates are registered on the Monomer Service). When the dataset reaches Ready, it opens on the dataset page.
Registration only adds monomers that are new to the Monomer Service. Monomers whose symbol already exists there are used as-is and are never overwritten or updated — so a library or SDF cannot change a monomer that other datasets already rely on. The service also runs a duplication check on structure: if the same monomer is already registered under a different symbol, it is matched to that existing entry (as an alias) rather than registered again.
If some peptides reference monomers that could not be resolved, they are imported with their HELM sequence preserved but without full structure or properties, and the dataset is flagged with a skipped-structures warning. See How to Resolve Missing Monomers.