---
name: lipid-maps-shorthand-notation
source: https://app.decimal.ai/s/lipid-maps-shorthand-notation@1/SKILL.md
source_sha256: 158fcfca8175
---

# LIPID MAPS shorthand notation

## Contract

Enforces the LIPID MAPS shorthand for mass-spectrometry-derived lipid names. The punctuation
carries meaning: the separator between chains, the prefixes, and the hydroxyl suffix each encode
exactly how much structure the measurement resolved. Apply whenever you write, normalize, or
correct a lipid species name for a results table, figure, or report.

## Rules

1. **Class then a single space then the composition.** Write `Class C:DB` — the class abbreviation,
   ONE space, then carbons`:`double-bonds. Never fuse them (`PC34:1`) and never wrap the composition
   in parentheses (`PC(34:1)`). `C` is total acyl/radyl carbons, `DB` total carbon-carbon double bonds.

2. **The chain separator states what was measured — this is the core of the convention:**
   - Chains identified but the sn-1 / sn-2 assignment NOT determined → join with an **underscore `_`**.
   - sn-1 / sn-2 genuinely assigned → join with a **slash `/`**, sn-1 chain written first.
   - **Only claim `/` when a regiochemistry-resolving method was run** (electron-activated dissociation,
     ozone-based, ultraviolet photodissociation, or an enzymatic assay). Ordinary collisional
     dissociation (CID) does NOT resolve sn — its acyl-loss intensities are a biased blend, not a
     structure readout — so default a CID-only name to `_`. When in doubt, drop a level.

3. **Sum-composition (species) level.** If the individual chains were never resolved, stop at
   `Class C:DB` (e.g. `PC 34:1`). Do not invent chains, an underscore, or a slash.

4. **Double-bond position + geometry** go in ONE pair of parentheses right after the chain: each a
   locant number followed by `Z` (cis) or `E` (trans), comma-separated for multiple bonds —
   `18:2(9Z,12Z)`. Never `cis`/`trans` words, `9c`/`9t`, a `Δ` delta symbol, or an `n-`/omega descriptor.

5. **Ether and plasmalogen linkages** use a radyl prefix directly before the chain: alkyl **ether = `O-`**,
   vinyl-ether **plasmalogen = `P-`** (e.g. `PC O-16:0/18:1`, `PE P-16:0/20:4`). The vinyl-ether double
   bond is implied by `P-` and is NOT counted in the chain's `DB`.

6. **Sphingoid-base hydroxylation** is a functional-group suffix `;O<n>` on the sphingoid part:
   `;O2` for a dihydroxy base (sphingosine/sphinganine), `;O3` for a trihydroxy base (phytosphingosine).
   The old `d`/`t` prefixes are deprecated — write `Cer 18:1;O2/24:0`, not `Cer d18:1/24:0`.

7. **Single-chain and other classes.** A lyso-lipid carries one acyl chain and no separator
   (`LPC 18:1`). Free fatty acids take the `FA` class token (`FA 18:0`), cholesteryl/sterol esters
   `CE` (`CE 18:1`). Added oxygens (hydroxyl/epoxide/keto) of unknown position are the same `;O<n>`
   suffix on the affected part (`FA 18:1;O` = one extra oxygen), consistent with the sphingoid rule.

The same six punctuation rules apply across every lipid category — glycerophospholipids, glycerolipids,
sphingolipids, sterols, and fatty acyls — so a name is portable between tools once it conforms.

## Worked examples (base default → conforming)

- `PC(34:1)` (parenthesized export) → `PC 34:1`
- `PC 16:0/18:1` claimed from CID-only data → `PC 16:0_18:1` (no sn evidence → underscore)
- `PC 16:0/18:1` with EAD sn assignment → `PC 16:0/18:1` (slash is licensed)
- `Cer d18:1/24:0` (old dihydroxy prefix) → `Cer 18:1;O2/24:0`
- `Cer t18:0/16:0` (old trihydroxy prefix) → `Cer 18:0;O3/16:0`
- `18:1 cis-9` / `18:1n-9` / `18:1Δ9` → `FA 18:1(9Z)`
- `plasmenyl-PE 18:0/20:4` → `PE P-18:0/20:4`
- `PC(O-16:0/18:1)` → `PC O-16:0/18:1`
- `LysoPC 18:1` / `1-oleoyl-LPC` → `LPC 18:1` (single acyl chain, no separator)
- `cholesteryl oleate` → `CE 18:1` (one acyl chain on the sterol)
- `18:1;OH (9-hydroxy, position unspecified)` → `FA 18:1;O` (functional-group oxygen suffix)

## Edge cases & exceptions

- **Ether vs plasmalogen at sum level:** a sum composition alone cannot distinguish `P-34:1` from
  `O-34:2` (a vinyl ether equals an ether plus one double bond). Report `O-` unless a vinyl-ether
  diagnostic ion or acid-lability test confirms `P-`.
- **`P-` double-bond bookkeeping:** because `P-` implies the enol double bond, `P-18:0` and `O-18:1`
  describe the same radyl; count only the additional double bonds under `P-`.
- **Geometry unmeasured:** if a double-bond position is known but its geometry is not, give the locant
  and omit the letter rather than guessing `Z`/`E`.
- **Odd or unexpected chains:** a name is a claim about evidence, not a guess — never promote a level
  (e.g. `_` to `/`) to look more precise.
- **Apparent odd-carbon species** (e.g. an odd total carbon count) are usually an in-source fragment or a
  ¹³C-isotope artifact of an even neighbor; do not name one as an intact species without chain confirmation.
- **Oxidized-lipid position** stated without evidence: use the bare `;O<n>` count rather than asserting a
  specific hydroxyl/epoxide locant the data did not localize.

## Do / Don't

- DO put a single space between class and composition. DON'T wrap it in parentheses.
- DO use `_` when the sn assignment is unproven. DON'T emit `/` without a regiochemistry-resolving method.
- DO write `;O2` / `;O3`. DON'T carry the old `d` / `t` sphingoid prefixes.
- DO encode double bonds as `(9Z)` / `(9E)`. DON'T write `cis`/`trans`, `9c`/`9t`, `Δ9`, or `n-9`.
- DO prefix ether with `O-` and plasmalogen with `P-`. DON'T spell out "alkyl", "plasmenyl", or "plasmalogen".

## Common mistakes

- Emitting a slash (`/`) when only the chain composition is known — the single most common overstatement.
- Carrying the deprecated `d18:1` / `t18:0` sphingoid prefixes instead of `;O2` / `;O3`.
- Writing double-bond geometry as `cis`/`trans` or with `Δ` / `n-` instead of `(nZ)` / `(nE)`.
- Wrapping the composition in parentheses (`PC(16:0/18:1)`) or fusing the class to the numbers.
- Inventing individual chains when only the summed composition was measured.

## Quick checklist

- [ ] class + single space + `C:DB` (no parentheses)
- [ ] `_` unless sn was truly resolved, then `/` with sn-1 first
- [ ] sum-composition only when chains unresolved (no invented `_`/`/`)
- [ ] `(nZ)` / `(nE)` for any double-bond position + geometry
- [ ] `O-` ether / `P-` plasmalogen prefix
- [ ] `;O2` / `;O3` sphingoid hydroxyl, never `d` / `t`