Spectral Retrieval and PubChem Atlas

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Query spectra

Paste one or more MS/MS spectra below. For multiple collision energies, click “Add another spectrum” and select the corresponding NCE (5–100%). The NCE will be converted to absolute eV using the precursor m/z computed from the formula and adduct.

If provided, spectra in the .ms file (one block per collision energy) will be parsed and used as query spectra. You can still edit the collision energy and peaks below.

Use spectra of a phospholipid standard (C27H56NO7P).

Uploads an MGF file (multiple features); select which feature to use as the query spectrum below. Metadata parsing is best-effort — please verify that the formula, adduct, and collision energy loaded correctly before running retrieval.

Spectrum 1
Helps remove electronic noise before computing entropy similarity.

Explore the atlas

Search by SMILES, compound name, InChI, InChIKey, or PubChem CID to view ICEBERG-predicted spectra from the precomputed atlas. Browse collision energies, hover substructure thumbnails to highlight peaks, and click a peak or thumbnail to see the predicted fragment.

🔖 Jump directly from a PubChem compound page (bookmarklet)
1
Show the bookmarks bar
Ctrl+Shift+B  /  ⌘⇧B
2
Drag the button below
up to your bookmarks bar
3
On any PubChem compound page,
click the bookmark
🔖 View in ICEBERG
↑ Drag this button to your bookmarks bar — don't click it here
Prefer to set it up manually?
  1. Right-click the bookmarks bar → Add page… (Chrome) or New Bookmark (Firefox).
  2. Set the Name to View in ICEBERG.
  3. Paste the following as the URL / Location:
javascript:(function(){var m=location.pathname.match(/\/compound\/(\d+)/);if(m){window.open('https://iceberg-ms.mit.edu/#explore?query='+m[1]+'&query_type=cid&src=pubchem');}else{var n=location.pathname.match(/\/compound\/([^\/\?#]+)/);if(n){window.open('https://iceberg-ms.mit.edu/#explore?query='+encodeURIComponent(n[1])+'&query_type=name&src=pubchem');}else{alert('No PubChem compound found in this page URL.');}}})();

No bookmarklet? You can also paste any PubChem CID number directly into the search box above — the Smart query type will detect it automatically.

Download predicted spectra (.mgf / .msp)

Download ICEBERG-predicted spectra for a specific PubChem formula from the atlas. You can either download the raw MGF only, or download MGF and a converted MSP file.
All NIST'23 structures are excluded to avoid license conflict. You can import the predicted library into your NIST MS Search software.

The current ICEBERG PubChem atlas contains 91,424,208 unique structures from PubChem.

SFTP Access
Browse the atlas with your WebUI email and password. The SFTP service is read-only and listens on port 2222. Available folders are /public/h_plus, /public/h_minus, and, for authorized accounts, /nist23/h_plus and /nist23/h_minus. Files are grouped by formula-derived C*, O*, and H* folders, for example C9/O4/H8/C9H8O4.mgf; formulas without those headers go under others. The layout is defined by get_formula_subdir. 
sftp -P 2222 -o User=your.email@domain.edu iceberg-ms.mit.edu
sshfs -p 2222 -o User=your.email@domain.edu iceberg-ms.mit.edu:/ ~/iceberg-atlas

Please cite:
Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry.
Runzhong Wang, Mrunali Manjrekar, Babak Mahjour, Julian Avila-Pacheco, Joules Provenzano, Erin Reynolds, Magdalena Lederbauer, Eivgeni Mashin, Samuel Goldman, Mingxun Wang, Jing-Ke Weng, Desirée L. Plata, Clary B. Clish, Connor W. Coley. bioRxiv 2025.
View the bioRxiv preprint

ICEBERG code: https://github.com/coleygroup/ms-pred

About ICEBERG

Inferring  Collision-induced-dissociation by  Estimating  Breakage  Events and  Reconstructing their  Graphs is a neural network model that predicts mass spectra from molecular structures. It can be used to elucidate unknown structures given mass spec.

ICEBERG model illustration
Coley Lab logo MIT Coley Group: https://coley.mit.edu/
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