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isobaric: wire verbs

The facts on this page are the same facts mzLibRust and mzLibR publish, because all three render them from one spec per wire verb. The parameter, result, error and caveat tables are generated; edit the spec, not this page. How the reference facts are generated explains the mechanism. For the Python signatures and result classes, see the API reference. For worked tasks, see the isobaric kits guide.

kits takes no file and makes no network call. Python's kits("TMT18") is the wire's --kit TMT18; with no argument every kit is listed. The result's kits field crosses as a list of {kit, channel_count} summaries, and Python's IsobaricKits.kits regroups the table under them.

kits

List the isobaric labelling kits mzLib can name, with every channel's label and reporter-ion m/z.

Wire verb isobaric kits · Python pymzlib.isobaric.kits

Wraps

Parameters

Parameter Type Default Unit Range Meaning
kit string absent — — One kit, resolved by mzLib's whole-name match, case-insensitive, optionally followed by " on ": TMT10, tmt10, TMT6-plex, iTRAQ-4plex on K. Never a substring, so TMT10plex is unknown. An unknown or blank name is a usage error naming the known kits. Absent: every kit.

Returns

Top-level fields:

Field Type Unit Null? Meaning
kit string — yes: --kit was not given: every kit is listed The --kit name exactly as given.
kit_count int kits never Kits listed.
record_count int channels never Rows in columns: the channels of every kit listed.
absolute_tolerance float Da never IsobaricMassTag.AbsoluteToleranceValue: the half-width of each channel's matching window.
kits object[] — never One per kit in IsobaricMassTagType order: {kit, channel_count}.
column_names string[] — never The table's columns in order.
columns table — never One row per (kit, channel), kits in enum order, channels in ascending m/z.
caveats string[] — never Five static caveats.

Per-row fields (one value per record, in columns or each list entry):

Field Type Unit Null? Meaning
kit string — never mzLib's IsobaricMassTagType member: TMT6, TMT10, TMT11, TMT16, TMT18, iTRAQ4, iTRAQ8, diLeu4, diLeu12 (at 0a808fec). TMT16 and TMT18 are TMTpro.
channel_index int — never 0-based position within the kit, ascending with reporter_ion_mz.
channel_label string — never The channel's name as MetaMorpheus spells it: 126, 127N, 127C, ..., 115a.
reporter_ion_mz float m/z never Theoretical m/z at charge 1: a DI HCD diagnostic-ion mass of the kit's Multiplex Label modification in mzLib's TMT.txt, plus one proton.
mz_min float m/z never reporter_ion_mz minus absolute_tolerance.
mz_max float m/z never reporter_ion_mz plus absolute_tolerance.

Errors

Kind pyMzLib raises When
usage UsageError --kit blank, or not a name mzLib knows (the message lists the kits)
correctness BridgeError mzLib cannot build a kit from its embedded modifications (never at 0a808fec)
service_unavailable ServiceUnavailableError never raised by this verb

Caveats

  • reporter_ion_mz is theoretical, charge 1, derived from mzLib's TMT.txt; not calibrated or observed.
  • mz_min and mz_max are mzLib's own reporter-ion matching window, the most intense peak inside it wins.
  • TMT16 is the lowest sixteen channels of TMTpro 18-plex and has no modification entry of its own.
  • iTRAQ8 has no 120 channel (the phenylalanine immonium ion sits at 120.081); its eighth reagent is 121.

Example

kits = pymzlib.isobaric.kits()

Recorded from the live bridge as isobaric_kits.json. The doctests in the API reference replay these recordings in CI.

tmtpro = pymzlib.isobaric.kits('TMT18')

Recorded from the live bridge as isobaric_kits_TMT18.json. The doctests in the API reference replay these recordings in CI.

Same verb in other bindings

Python (pyMzLib) Rust (mzLibRust) R (mzLibR)
pymzlib.isobaric.kits mzlib::isobaric::kits isobaric_kits

References

  • doi:10.1021/acs.jproteome.1c00168: the TMTpro-18plex reagents paper (Li et al. 2021); mzLib cites it as the source of its 0.003 Da reporter-ion matching tolerance (IsobaricMassTag.AbsoluteToleranceValue, IsobaricMassTag.cs:41)

Since

Wire protocol pyMzLib mzLibRust mzLibR
1 0.3.0 not yet shipped not yet shipped

Not yet verified

  • A second verb could read reporter intensities out of spectra through IsobaricMassTag.GetReporterIonIntensities; not built.
  • Not yet ported: mzLibRust and mzLibR names above are proposals until their ports land (parity order).