Instrument-specific tables

Acquisition-mode-specific tables documented and verified against the probe corpus.

DIA / diaPASEF

Presence: DiaFrameMsMsWindows + DiaFrameMsMsInfo + DiaFrameMsMsWindowGroups. Verified against PXD025576 (sv=3.1, DIAMAX method, codec=2, ScanMode=9).

PASEF DDA bundles (ScanMode=8) include these tables but leave them empty. diaPASEF bundles (ScanMode=9) have PasefFrameMsMsInfo and Precursors absent entirely; isolation metadata lives entirely in the DIA tables.

DiaFrameMsMsInfo - one row per MS2 frame:

Frame        INTEGER  frame ID (FK into Frames; only ScanMode=9, MsMsType=9 frames)
WindowGroup  INTEGER  FK into DiaFrameMsMsWindowGroups.Id

DiaFrameMsMsWindowGroups - registry of window group IDs:

Id  INTEGER  primary key

DiaFrameMsMsWindows - isolation windows within a group:

WindowGroup     INTEGER  FK into DiaFrameMsMsWindowGroups.Id
ScanNumBegin    INTEGER  first scan of this isolation window (inclusive)
ScanNumEnd      INTEGER  last scan of this isolation window (inclusive)
IsolationMz     REAL     centre m/z of the precursor isolation window
IsolationWidth  REAL     full width of the isolation window (Da)
CollisionEnergy REAL     collision energy (eV) applied during this window

In a diaPASEF acquisition each window group has multiple rows that tile the full scan (1/K0) range. Within a group the scan ranges are non-overlapping and contiguous. The isolation m/z steps across groups so that the product of groups x windows-per-group covers the full targeted m/z range.

Sample data (PXD025576, DIAMAX, 16 groups x 4 windows = 64 rows total):

-- window group 1
(1,   0, 268, 1012.5, 25.0, 53.68)
(1, 269, 440,  812.5, 25.0, 42.08)
(1, 441, 611,  612.5, 25.0, 33.02)
(1, 612, 774,  412.5, 25.0, 24.22)
-- window group 2
(2,   0, 256, 1037.5, 25.0, 54.00)
(2, 257, 425,  837.5, 25.0, 42.77)
...

The 1/K0-m/z co-isolation pattern (higher m/z at higher 1/K0) exploits the natural correlation between peptide charge state, m/z, and ion mobility, minimising chimeric spectra. CollisionEnergy scales with IsolationMz to optimise fragmentation across the m/z range.

DiaFrameMsMsInfo links each MS2 frame to one window group. The 16 groups cycle continuously (frames 2-17 use groups 1-16, frames 18-33 repeat, ...). MS1 frames (MsMsType=0) have no entry in DiaFrameMsMsInfo.

PASEF DDA

Presence: PasefFrameMsMsInfo + Precursors.

PasefFrameMsMsInfo - one row per MS2 scan range within a PASEF frame:

Frame           INTEGER  frame ID (FK into Frames)
ScanNumBegin    INTEGER  first scan isolating this precursor (inclusive)
ScanNumEnd      INTEGER  last scan isolating this precursor (inclusive)
IsolationMz     REAL     centre m/z of isolation window
IsolationWidth  REAL     full width of isolation window (Da)
CollisionEnergy REAL     collision energy (eV)
Precursor       INTEGER  FK into Precursors.Id

Sample rows (PXD027359, sv=3.5, 87138 total rows):

(2, 566, 591, 621.082, 2.0, 35.172, 1)
(2, 720, 745, 353.903, 2.0, 28.438, 2)
(2, 775, 800, 281.178, 2.0, 26.034, 3)

Precursors - one row per detected precursor ion:

Id              INTEGER  primary key
LargestPeakMz   REAL     m/z of the most intense isotopologue
AverageMz       REAL     intensity-weighted average m/z
MonoisotopicMz  REAL     monoisotopic m/z (NULL if not determined)
Charge          INTEGER  charge state (NULL if not determined)
ScanNumber      REAL     centroid scan (fractional; maps to 1/K0)
Intensity       REAL     summed precursor intensity
Parent          INTEGER  parent MS1 frame ID

MonoisotopicMz and Charge are NULL when the deconvolution algorithm cannot determine them (common for low-intensity or co-eluting precursors).

prm-PASEF

Verified against PXD028279 (Brzhozovskiy et al., Anal. Chem. 2022; prm-PASEF on timsTOF Pro, sv=3.5, timsControl 2.0.18.0). The .d bundle contains 26,171 MS1 frames and 10,570 PRM frames (MsMsType=10, ScanMode=10) against 250 scheduled targets.

PRM frames have MsMsType=10 and ScanMode=10 in Frames. The DiaFrameMsMsInfo table is empty (diaPASEF and PRM are mutually exclusive within an acquisition).

PrmFrameMsMsInfo (34,418 rows in PXD028279):

Frame           INTEGER  FK into Frames.Id; each PRM frame has one row per active target
ScanNumBegin    INTEGER  first scan index of the isolation window
ScanNumEnd      INTEGER  last scan index of the isolation window
IsolationMz     REAL     precursor m/z centre of the isolation window
IsolationWidth  REAL     isolation window width in Da (3.0 in PXD028279)
CollisionEnergy REAL     collision energy in eV
Target          INTEGER  FK into PrmTargets.Id

Multiple rows per frame are expected when more than one target is measured per frame.

PrmTargets (250 rows in PXD028279):

Id              INTEGER  primary key
ExternalId      TEXT     user-supplied target label (e.g. peptide name or compound ID)
Time            REAL     scheduled retention time (min)
OneOverK0       REAL     expected inverse ion mobility (1/K0)
MonoisotopicMz  REAL     monoisotopic precursor m/z
Charge          INTEGER  precursor charge state
Description     TEXT     free-text annotation

PrmFrameMeasurementMode (10,570 rows in PXD028279):

Frame             INTEGER  FK into Frames.Id
MeasurementModeId TEXT     measurement-mode identifier; NULL in all observed rows

All 10,570 rows have MeasurementModeId = NULL in PXD028279. The column presumably encodes online vs offline measurement-mode switching, but no non-NULL value has been observed.

PrmFrameMsMsInfo and PrmTargets are present in 54 of 64 probe corpus bundles (spanning sv 3.1 to 3.7) but are always empty when PRM is not active.

Legacy DDA (FrameMsMsInfo)

Presence: all acquisitions (all 64 probe corpus bundles). Always empty. Superseded by PasefFrameMsMsInfo for PASEF DDA and by the Dia* tables for diaPASEF.

Frame           INTEGER  frame ID
Parent          INTEGER  parent MS1 frame ID
TriggerMass     REAL     precursor trigger mass
IsolationWidth  REAL     isolation window width
PrecursorCharge INTEGER  charge state (0 = unassigned)
CollisionEnergy REAL     collision energy

CalibrationInfo

Presence: all acquisitions.

KeyPolarity  TEXT  polarity qualifier, "+" or "-" (dual-polarity bundles have both)
KeyName      TEXT  parameter name (see below)
Value        BLOB  parameter value (TEXT or binary IEEE-754 double array)

Observed KeyName values (PXD027359):

KeyName	Value type	Example
CalibrationDateTime	TEXT	2020-12-04T11:41:21+01:00
CalibrationUser	TEXT	Demo User
CalibrationSoftware	TEXT	timsTOF
CalibrationSoftwareVersion	TEXT	2.0.40
MzCalibrationMode	TEXT of int	4
MzStandardDeviationPPM	TEXT of float	0.325020
ReferenceMassList	TEXT	TuneMixIsotopes_ADB
ReferencePeakMasses	binary f64[]	packed little-endian doubles
MeasuredTimesOfFlight	binary f64[]	measured TOF values for reference peaks
MeasuredMassPeakIntensities	binary f64[]	intensities of reference peaks
MassesCorrectedCalibration	binary f64[]	post-calibration m/z values
MobilityCalibrationDateTime	TEXT	2020-12-08T08:28:39+00:00
MobilityStandardDeviationPercent	TEXT of float	1410.782798
ReferenceMobilityList	TEXT	Tuning Mix ES-TOF (ESI)
ReferencePeakMobilities	binary f64[]	reference 1/K0 values
MeasuredTimsVoltages	binary f64[]	measured TIMS voltages for reference peaks

Binary blobs are arrays of little-endian f64 (IEEE-754 double) values; len_bytes / 8 is the number of reference peaks.

MeasuredTimesOfFlight is in ns. The MzCalibration row of the same polarity maps it to MassesCorrectedCalibration; see 04-calibration.md.

FrameProperties / PropertyDefinitions

Presence: all acquisitions (sv >= 3.1).

FrameProperties:

Frame     INTEGER  frame ID
Property  INTEGER  FK into PropertyDefinitions.Id
Value     REAL     measured value in units given by PropertyDefinitions

PropertyDefinitions:

Id                INTEGER  property ID
PermanentName     TEXT     machine-readable name
Type              INTEGER  0 = enum/integer, 1 = real-valued
DisplayGroupName  TEXT     UI group (e.g. "Source", "Vacuum", "Digitizer")
DisplayName       TEXT     human-readable name
DisplayValueText  TEXT     enum legend for Type=0
DisplayFormat     TEXT     printf-style format string
DisplayDimension  TEXT     unit string
Description       TEXT     additional description

Representative properties observed across the corpus:

PermanentName	DisplayName	Unit
Source_NebulizerCurrentValue	Nebulizer	Bar
Source_NanoBoosterCurrentValue	nanoBooster	Bar
Source_DryGasCurrentValue	Dry Gas	l/min
Source_DryHeaterCurrentValue	Dry Heater	degC
Source_CapillaryCurrentValue	Capillary	nA
Vacuum_CurrentFore	Tunnel Out Vacuum	mBar
Vacuum_CurrentHigh	TOF Vacuum	mBar
Digitizer_CurrentTemp	Digitizer Temperature	degC
Digitizer_Summation	Summation	x
SpectraAcquisition_SegmentId	Segment Id	-

Property IDs are not stable across schema versions (sv 3.1 / 3.3 use IDs in the 1000+ range; sv 3.5 / 3.7 use IDs starting at 0). Always resolve via a PropertyDefinitions.Id join. FrameProperties is informational instrument telemetry and is not required for peak decoding.

GroupProperties stores per-acquisition-group set-point values (instrument configuration), analogous to FrameProperties but keyed by property group rather than by frame.

PropertyGroup  INTEGER             FK into PropertyGroups.Id
Property       INTEGER             FK into PropertyDefinitions.Id
Value          (no type affinity)  value (stored as INTEGER or REAL)

PropertyGroups registers the available group IDs:

Id  INTEGER  primary key

All 64 probe corpus bundles have exactly one PropertyGroup (Id=1). Across the corpus 1077 unique property IDs appear in GroupProperties, in categories spanning IMS, MSMS, Transfer, Calibration, TOF, Digitizer, SyringePump, Source, Collision, Energy, Quadrupole, and others.

CollisionEnergySweepingInfo

Presence: sv >= 3.7 only.

Frame                  INTEGER  frame ID
CollisionId            INTEGER  CE step index within the sweep (0-based)
CollisionEnergy        REAL     absolute collision energy (eV)
CollisionEnergyPercent REAL     CE as a fraction of the m/z-dependent optimal CE

Present in all sv=3.7 bundles by schema but never populated in any publicly accessible PRIDE dataset. Checked across 81 distinct .d bundles spanning sv 3.1-3.7: every bundle has 0 rows. The column names suggest it is intended for stepped-CE acquisition modes where multiple discrete CE values are applied per frame.

Segments

Presence: all acquisitions.

Id                   INTEGER  primary key, 1-based
FirstFrame           INTEGER  first frame ID in this segment
LastFrame            INTEGER  last frame ID in this segment
IsCalibrationSegment BOOLEAN  1 if this is a dedicated calibration segment

In all 64 probe corpus bundles there is exactly one row, covering the full acquisition, with IsCalibrationSegment = 0. Multi-segment and calibration-segment acquisitions are supported by the schema but were not observed in the corpus.

ErrorLog

Presence: all acquisitions. Usually empty.

Frame    INTEGER  frame ID where the condition occurred
Scan     INTEGER  scan index within the frame (NULL for frame-level events)
Message  TEXT     compact message string

Populated in only one bundle observed (PXD022216, sv=3.1, codec=1, diaPASEF, 2 rows). The "I:" prefix appears to denote "Info" severity; no "W:" or "E:" prefixes were observed.

MALDI (MaldiFrameInfo)

MALDI timsTOF acquisitions produce analysis.tsf bundles, not analysis.tdf. The .tsf format uses a different SQLite schema and binary data layout and is out of scope for this crate. See 06-references-and-gaps.md.