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SequalJS

SequalJS is a JavaScript/TypeScript library for parsing and manipulating ProForma peptide sequence notation. It allows handling protein and peptide sequences with modifications, useful for proteomics research, mass spectrometry data analysis, and bioinformatics applications.

Features

  • Full support for ProForma 2.0 and ProForma 2.1 standards for proteoform notation
  • Parse complex peptide sequences with modifications
  • Handle various modification types:
    • Site-specific modifications
    • Terminal modifications (N-terminal and C-terminal)
    • Global modifications
    • Mass shift modifications
    • Labile modifications
    • Modifications with unknown positions
  • Support for advanced ProForma features:
    • INFO tags and metadata
    • Ambiguity groups with localization scores
    • Sequence ambiguities
    • Crosslinks and branches
    • Range modifications
  • ProForma 2.1 features:
    • Charged formulas (Section 11.1)
    • Ion notation for fragment ions (Section 11.6)
    • Placement controls (Position, Limit, CoMKP, CoMUP) (Section 11.2)
    • Named entities (peptidoform, peptidoform ion, compound ion) (Section 8.2)
    • Custom monosaccharides in glycan notation (Section 10.2)
    • Terminal-specific global modifications (Section 11.3.2)
  • Precise handling of decimal values in mass shifts

Installation

npm install sequaljs

Usage

Basic Parsing

import { Sequence } from 'sequaljs/dist/sequence';

// Parse a simple peptide with modification
const seq = Sequence.fromProforma('ELVIS[Phospho]K');
console.log(seq.seq[4].value); // "S"
console.log(seq.seq[4].mods[0].modValue.primaryValue); // "Phospho"

// Convert back to ProForma notation
console.log(seq.toProforma()); // "ELVIS[Phospho]K"

Terminal Modifications

import { Sequence } from 'sequaljs/dist/sequence';

// N-terminal and C-terminal modifications
const seq = Sequence.fromProforma('[Acetyl]-PEPTIDE-[Amidated]');

// Access N-terminal modification (position -1)
const nTermMod = seq.mods.get(-1);
if (nTermMod) {
  console.log(nTermMod[0].modValue.primaryValue); // "Acetyl"
}

// Access C-terminal modification (position -2)
const cTermMod = seq.mods.get(-2);
if (cTermMod) {
  console.log(cTermMod[0].modValue.primaryValue); // "Amidated"
}

Global Modifications

import { Sequence } from 'sequaljs/dist/sequence';

// Global fixed modification
const seq = Sequence.fromProforma('<[Carbamidomethyl]@C>PEPTCDE');
console.log(seq.globalMods[0].modValue.primaryValue); // "Carbamidomethyl"
console.log(seq.globalMods[0].targetResidues); // ["C"]

Working with INFO Tags

import { Sequence } from 'sequaljs/dist/sequence';

// Parse sequence with INFO tag
const seq = Sequence.fromProforma('ELVIS[Phospho|INFO:newly discovered]K');
const mod = seq.seq[4].mods[0];
console.log(mod.modValue.primaryValue); // "Phospho"
console.log(mod.infoTags[0]); // "newly discovered"

// Multiple INFO tags
const seq2 = Sequence.fromProforma('ELVIS[Phospho|INFO:newly discovered|INFO:Created on 2021-06]K');
console.log(seq2.seq[4].mods[0].infoTags.length); // 2
console.log(seq2.seq[4].mods[0].infoTags); // ["newly discovered", "Created on 2021-06"]

Joint Representation

import { Sequence } from 'sequaljs/dist/sequence';

// Parse sequence with joint interpretation and mass
const seq = Sequence.fromProforma('ELVIS[U:Phospho|+79.966331]K');
const mod = seq.seq[4].mods[0];
console.log(mod.modValue.primaryValue); // "Phospho"
console.log(mod.source); // "U"
console.log(mod.modValue.pipeValues[1].mass); // 79.966331

// With observed mass
const seq2 = Sequence.fromProforma('ELVIS[U:Phospho|Obs:+79.978]K');
const mod2 = seq2.seq[4].mods[0];
console.log(mod2.modValue.primaryValue); // "Phospho"
console.log(mod2.modValue.pipeValues[1].observedMass); // 79.978

Crosslinks and Complex Features

import { Sequence } from 'sequaljs/dist/sequence';

// Crosslinks with mass shifts and info tags
const seq = Sequence.fromProforma('PEPTK[XL:DSS#XL1|+138.068|INFO:reaction=NHS]IDE');
const mod = seq.seq[4].mods[0];
console.log(mod.modValue.primaryValue); // "DSS"
console.log(mod.source); // "XL"
console.log(mod.crosslinkId); // "XL1"
console.log(mod.modValue.pipeValues[1].mass); // 138.068
console.log(mod.infoTags[0]); // "reaction=NHS"

// Complex example with multiple modification types
const complex = Sequence.fromProforma(
  'PEP[U:Deamidation|+0.984]T[U:Phospho#1(0.75)|+79.966]K[XL:DSS#XL2]IDE'
);

Gap Notation

import { Sequence } from 'sequaljs/dist/sequence';

// Parse sequence with gap of known mass
const seq = Sequence.fromProforma('RTAAX[+367.0537]WT');
console.log(seq.toStrippedString()); // "RTAAXWT"
console.log(seq.seq[4].value); // "X"
console.log(seq.seq[4].mods[0].modType); // "gap"
console.log(seq.seq[4].mods[0].mass); // 367.0537

Charged Peptides

import { Sequence } from 'sequaljs/dist/sequence';

// Parse a peptide with charge state
const seq = Sequence.fromProforma('PEPTIDE/2');
console.log(seq.charge); // 2

// Parse a peptide with modification and charge state
const seq2 = Sequence.fromProforma('ELVIS[Phospho]K/3');
console.log(seq2.charge); // 3
console.log(seq2.toProforma()); // "ELVIS[Phospho]K/3"

// Modify charge state
seq2.charge = 4;
console.log(seq2.toProforma()); // "ELVIS[Phospho]K/4"

// Peptide with ionic species
const seq3 = Sequence.fromProforma('PEPTIDE/2[+Na+]');
console.log(seq3.charge); // 2
console.log(seq3.ionicSpecies); // "+Na+"

Chimeric Spectra

import { Sequence } from 'sequaljs/dist/sequence';

// Parse a basic chimeric spectrum with two peptides
const chimeric = Sequence.fromProforma('PEPTIDE/2+ANOTHER/3');
console.log(chimeric.isChimeric); // true
console.log(chimeric.toStrippedString()); // "PEPTIDE" (first component)
console.log(chimeric.peptidoforms.length); // 2
console.log(chimeric.charge); // 2
console.log(chimeric.peptidoforms[1].toStrippedString()); // "ANOTHER"
console.log(chimeric.peptidoforms[1].charge); // 3

// Complex chimeric spectrum with modifications
const complexChimeric = Sequence.fromProforma(
  '[Acetyl]-PEP[+79.966]TIDE-[Amidated]/2[+Na+]+S[Phospho]EQ/3'
);
console.log(complexChimeric.peptidoforms.length); // 2
console.log(complexChimeric.mods.get(-1)[0].modValue.primaryValue); // "Acetyl"
console.log(complexChimeric.seq[2].mods[0].modValue.primaryValue); // "+79.966"
console.log(complexChimeric.ionicSpecies); // "+Na+"
console.log(complexChimeric.peptidoforms[1].seq[0].mods[0].modValue.primaryValue); // "Phospho"

ProForma 2.1 Features

Charged Formulas

import { Sequence } from 'sequaljs/dist/sequence';

// Charged formula notation
const seq = Sequence.fromProforma('PEPT[Formula:C2H3NO:z-1]IDE');
const mod = seq.seq[3].mods[0];
console.log(mod.modValue.source); // "Formula"
console.log(mod.modValue.primaryValue); // "C2H3NO"
console.log(mod.modValue.chargeValue); // -1

// Multiple charged formulas
const seq2 = Sequence.fromProforma('PEPT[Formula:C2H3NO:z-1]IDE[Formula:Zn1:z+2]K');
console.log(seq2.seq[3].mods[0].modValue.chargeValue); // -1
console.log(seq2.seq[6].mods[0].modValue.chargeValue); // 2

Ion Notation

import { Sequence } from 'sequaljs/dist/sequence';

// Fragment ion notation
const seq = Sequence.fromProforma('PEPTIDE-[b-type-ion]');
const cTermMod = seq.mods.get(-2);
console.log(cTermMod[0].isIonType); // true
console.log(cTermMod[0].modValue.primaryValue); // "b-type-ion"

// Multiple ion types
const seq2 = Sequence.fromProforma('[a-type-ion]-PEPTIDE-[y-type-ion]');
console.log(seq2.mods.get(-1)[0].isIonType); // true
console.log(seq2.mods.get(-2)[0].isIonType); // true

Placement Controls

import { Sequence } from 'sequaljs/dist/sequence';

// Position constraint
const seq = Sequence.fromProforma('<[TMT6plex|Position:M,C]@K>MTPEILTCNSIGCLKG');
console.log(seq.globalMods[0].positionConstraint); // ["M", "C"]

// Limit per position
const seq2 = Sequence.fromProforma('<[Oxidation|Limit:2]@M>MMMMMMMM');
console.log(seq2.globalMods[0].limitPerPosition); // 2

// Colocalization constraints
const seq3 = Sequence.fromProforma('<[Phospho|CoMKP]@S,T,Y>STYPEPTIDE');
console.log(seq3.globalMods[0].colocalizeKnown); // true

const seq4 = Sequence.fromProforma('<[Oxidation|CoMUP]@M>MMMPEPTIDE');
console.log(seq4.globalMods[0].colocalizeUnknown); // true

// Combined placement controls
const seq5 = Sequence.fromProforma(
  '<[TMT6plex|Position:M,C|Limit:1|CoMKP]@K,N-term>MTPEILTCNSIGCLKG'
);
console.log(seq5.globalMods[0].positionConstraint); // ["M", "C"]
console.log(seq5.globalMods[0].limitPerPosition); // 1
console.log(seq5.globalMods[0].colocalizeKnown); // true

Named Entities

import { Sequence } from 'sequaljs/dist/sequence';

// Peptidoform name
const seq = Sequence.fromProforma('(>TMT-labeled peptide)PEPTIDEK');
console.log(seq.peptidoformName); // "TMT-labeled peptide"

// Peptidoform ion name
const seq2 = Sequence.fromProforma('(>>Precursor z=2)PEPTIDEK/2');
console.log(seq2.peptidoformIonName); // "Precursor z=2"
console.log(seq2.charge); // 2

// Compound ion name
const seq3 = Sequence.fromProforma('(>>>Chimeric Spectrum 1234)PEPTIDEK/2');
console.log(seq3.compoundIonName); // "Chimeric Spectrum 1234"

// All three naming levels
const seq4 = Sequence.fromProforma(
  '(>>>Chimeric Spectrum 1234)(>>Precursor z=2)(>Phospho-peptide)PEPS[Phospho]T/2'
);
console.log(seq4.compoundIonName); // "Chimeric Spectrum 1234"
console.log(seq4.peptidoformIonName); // "Precursor z=2"
console.log(seq4.peptidoformName); // "Phospho-peptide"

Custom Monosaccharides in Glycans

import { Sequence } from 'sequaljs/dist/sequence';

// Custom monosaccharide notation
const seq = Sequence.fromProforma('N[Glycan:{C8H13N1O5}1Hex2]PEPTIDE');
const mod = seq.seq[0].mods[0];
console.log(mod.modValue.source); // "Glycan"
console.log(mod.modValue.isValidGlycan); // true

// Labile custom monosaccharides
const seq2 = Sequence.fromProforma('{Glycan:{C8H13N1O5}1Hex2}PEPTIDE');
const labileMods = seq2.mods.get(-3);
console.log(labileMods[0].modValue.source); // "Glycan"

// Mixed custom and standard monosaccharides
const seq3 = Sequence.fromProforma('N[Glycan:{C11H17N1O9}2Hex3HexNAc2]PEPTIDE');
console.log(seq3.seq[0].mods[0].modValue.isValidGlycan); // true

// Custom monosaccharides with isotopes
const seq4 = Sequence.fromProforma('N[Glycan:{C8H13[15N1]O5}2Hex1]PEPTIDE');
console.log(seq4.seq[0].mods[0].modValue.isValidGlycan); // true

Terminal-Specific Global Modifications

import { Sequence } from 'sequaljs/dist/sequence';

// N-terminal specific global modification
const seq = Sequence.fromProforma('<[TMT6plex]@N-term>PEPTIDEK');
console.log(seq.globalMods[0].targetResidues); // [{"type": "terminal", "terminal": "N-term"}]

// C-terminal specific global modification
const seq2 = Sequence.fromProforma('<[Amidated]@C-term>PEPTIDEK');
console.log(seq2.globalMods[0].targetResidues); // [{"type": "terminal", "terminal": "C-term"}]

// Terminal-specific with amino acid constraint
const seq3 = Sequence.fromProforma('<[Gln->pyro-Glu]@N-term:Q>QPEPTIDE');
console.log(seq3.globalMods[0].targetResidues);
// [{"type": "terminal_specific", "terminal": "N-term", "aminoAcid": "Q"}]

// Multiple targets including terminals
const seq4 = Sequence.fromProforma('<[TMT6plex]@K,N-term>PEPTIDEK');
console.log(seq4.globalMods[0].targetResidues);
// ["K", {"type": "terminal", "terminal": "N-term"}]

// Complex terminal global modifications
const seq5 = Sequence.fromProforma(
  '<[Acetyl]@N-term><[Oxidation]@M,C-term:G>MTPEILTCNSIGCLKG'
);
console.log(seq5.globalMods.length); // 2
console.log(seq5.globalMods[1].targetResidues);
// ["M", {"type": "terminal_specific", "terminal": "C-term", "aminoAcid": "G"}]

API Reference

Core Methods

  • Sequence.fromProforma(string): Parse a ProForma string into a Sequence object
  • Sequence.toProforma(): Convert a Sequence object back to a ProForma string
  • Sequence.toStrippedString(): Get the plain amino acid sequence without modifications

Properties

  • Sequence.seq: Access the individual residues with their modifications
  • Sequence.mods: Access modifications by position, including terminal modifications
    • Position -1: N-terminal modifications
    • Position -2: C-terminal modifications
    • Position -3: Labile modifications
    • Position -4: Unknown position modifications
  • Sequence.globalMods: Access global modifications
  • Sequence.sequenceAmbiguities: Access sequence ambiguity information
  • Sequence.charge: Charge state of the peptide
  • Sequence.ionicSpecies: Ionic species (e.g., "+Na+", "+K+")
  • Sequence.isChimeric: Boolean indicating if this is a chimeric spectrum
  • Sequence.peptidoforms: Array of component peptides in chimeric spectra

ProForma 2.1 Properties

  • Sequence.peptidoformName: Name of the peptidoform (single > prefix)
  • Sequence.peptidoformIonName: Name of the peptidoform ion (double >> prefix)
  • Sequence.compoundIonName: Name of the compound ion (triple >>> prefix)

Modification Properties

  • Modification.modValue.chargeValue: Charge value for charged formulas
  • Modification.isIonType: Boolean indicating if this is an ion type modification
  • Modification.positionConstraint: Position constraint for placement controls
  • Modification.limitPerPosition: Limit per position for placement controls
  • Modification.colocalizeKnown: Colocalize with known peptidoforms flag
  • Modification.colocalizeUnknown: Colocalize with unknown peptidoforms flag

Global Modification Properties

  • GlobalModification.targetResidues: Array of target residues (can include terminal targets)
    • String values: amino acid codes (e.g., "K", "M")
    • Object values for terminals: {"type": "terminal", "terminal": "N-term" | "C-term"}
    • Object values for terminal-specific: {"type": "terminal_specific", "terminal": "N-term" | "C-term", "aminoAcid": string}

License

MIT

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JavaScript/TypeScript library for parsing and manipulating ProForma peptide sequence notation

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