Reference molecules

About

The mzPAF specification uses specification/reference_data/reference_molecules.json as auxiliary reference data. In this way, the set of reference molecules can be extended without updating the specification document itself.

The following files are available:

• reference_molecules.json: Software parsable list of “reference molecules” often seen in peptide fragmentation spectra, but not normal peptide fragments. This includes isobaric labeling reagent related molecules, monosaccharides, nucleotides, etc. These molecules may be individual charged ions (typically protonated), or may be used as neutral losses as appropriate.

• reference_molecule_schema.json: JSON schema defining the structure of the JSON file

See Reference molecule ions in the specification document for more information.

Reference molecule table

The following analytes can be annotated as reference molecules with the r prefix and the listed name between square brackets (e.g. r[TMT127N]).

	label_type	molecule_type	chemical_formula	ion_mz	neutral_mass
TMT126	TMT	reporter	C8N1H15	126.128
TMT127N	TMT	reporter	C8[15N1]H15	127.125
TMT127C	TMT	reporter	C7[13C1]N1H15	127.131
TMT128N	TMT	reporter	C7[13C1][15N1]H15	128.128
TMT128C	TMT	reporter	C6[13C2]N1H15	128.134
TMT129N	TMT	reporter	C6[13C2][15N1]H15	129.131
TMT129C	TMT	reporter	C5[13C3]N1H15	129.138
TMT130N	TMT	reporter	C5[13C3][15N1]H15	130.135
TMT130C	TMT	reporter	C4[13C4]N1H15	130.141
TMT131N	TMT	reporter	C4[13C4][15N1]H15	131.138
TMT131C	TMT	reporter	C3[13C5]N1H15	131.144
TMT132N	TMT	reporter	C3[13C5][15N1]H15	132.142
TMT132C	TMT	reporter	C2[13C6]N1H15	122.148
TMT133N	TMT	reporter	C2[13C6][15N1]H15	133.145
TMT133C	TMT	reporter	C1[13C7]N1H15	133.151
TMT134N	TMT	reporter	C1[13C7][15N1]H15	134.148
TMT134C	TMT	reporter	[13C8]N1H15	134.155
TMT135N	TMT	reporter	[13C8][15N1]H15	135.152
TMTzero	TMTzero	reporter+balance	C12H20N2O2	225.16	224.152
TMTpro_zero	TMTpro_zero	reporter+balance	C15H25N3O3	296.197	295.19
TMT2plex	TMT2plex	reporter+balance	C11[13C1]H20N2O2	226.163	225.156
TMT6plex	TMT6plex	reporter+balance	C8[13C5]H20N1[15N1]O2	230.17	229.163
TMTpro	TMTpro	reporter+balance	C8[13C7]H25[15N2]N1O3	305.214	304.207
iTRAQ113	iTRAQ	reporter	C6N2H12	113.108
iTRAQ114	iTRAQ	reporter	C5[13C1]N2H12	114.111
iTRAQ115	iTRAQ	reporter	C5[13C1]N1[15N1]H12	115.108
iTRAQ116	iTRAQ	reporter	C4[13C2]N1[15N1]H12	116.112
iTRAQ117	iTRAQ	reporter	C3[13C3]N1[15N1]H12	117.115
iTRAQ118	iTRAQ	reporter	C3[13C3][15N2]H12	118.112
iTRAQ119	iTRAQ	reporter	C2[13C4][15N2]H12	119.115
iTRAQ121	iTRAQ	reporter	[13C6][15N2]H12	121.122
iTRAQ4plex	iTRAQ4plex	reporter+balance	C4[13C3]N1[15N1]O1H12	145.109	144.102
iTRAQ8plex	iTRAQ8plex	reporter+balance	C7[13C7]N3[15N1]O3H24	305.213	304.205
TMT126-ETD	TMT	reporter	C7N1H15	114.128
TMT127N-ETD	TMT	reporter	C7[15N1]H15	115.125
TMT127C-ETD	TMT	reporter	C6[13C1]N1H15	114.128
TMT128N-ETD	TMT	reporter	C6[13C1][15N1]H15	115.125
TMT128C-ETD	TMT	reporter	C5[13C2]N1H15	116.134
TMT129N-ETD	TMT	reporter	C5[13C2][15N1]H15	117.131
TMT129C-ETD	TMT	reporter	C4[13C3]N1H15	116.134
TMT130N-ETD	TMT	reporter	C4[13C3][15N1]H15	117.131
TMT130C-ETD	TMT	reporter	C3[13C4]N1H15	118.141
TMT131N-ETD	TMT	reporter	C3[13C4][15N1]H15	119.138
TMT131C-ETD	TMT	reporter	C2[13C5]N1H15	118.141
sidechain_A		sidechain	C1H3		15.0235
sidechain_C		sidechain	C1H3S1		46.9955
sidechain_D		sidechain	C2H2O2		58.0055
sidechain_E		sidechain	C3H4O2		72.0211
sidechain_F		sidechain	C7H7		91.0548
sidechain_G		sidechain	H1		1.00782
sidechain_H		sidechain	C4H5N2		81.0453
sidechain_I		sidechain	C4H9		57.0704
sidechain_J		sidechain	C4H9		57.0704
sidechain_K		sidechain	C4H10N1		72.0813
sidechain_L		sidechain	C4H9		57.0704
sidechain_M		sidechain	C3H7S1		75.0268
sidechain_N		sidechain	C2H4N1O1		58.0293
sidechain_O		sidechain	C9H17N2O1		169.134
sidechain_Q		sidechain	C3H6N1O1		72.0449
sidechain_R		sidechain	C4H10N3		100.087
sidechain_S		sidechain	C1H3O1		31.0184
sidechain_T		sidechain	C2H5O1		45.034
sidechain_U		sidechain	C1H3Se1		94.94
sidechain_V		sidechain	C3H7		43.0548
sidechain_W		sidechain	C9H8N1		130.066
sidechain_Y		sidechain	C7H7O1		107.05

JSON schema

The reference_molecules.json file is defined by the following schema:

Pattern Properties

• .{1,}: Refer to #/definitions/molecule.

Definitions

• molecule (object): A single molecule that may be present as a reporter ion or signature ion, or be a component of a neutral loss.

  • name (string): The formal name for this molecule by which it should be referenced.

  • cv_term (array)

    • Items (string)

  • neutral_mass (number): The neutral mass of the molecule not including any charge or charge carrier.

  • molecule_type (string): A categorical label for this molecule.

    Examples:

    "monosaccharide"
    

    "reporter"
    

    "reporter+balance"
    

  • ion_mz (number): The m/z of the molecule if it is expected to be reasonably different from the uncharged version.

  • chemical_formula (string): The elemental formula of the neutral molecule.

  • ion_chemical_formula (string): The chemical formula of the charged molecule.

  • references (array): An array of sources and references describing this entity.

    • Items (string)