Scan Events

ScanEvent, ScanEventPreamble, Reaction, FractionCollector

21. ScanEvent

Describes the type and parameters of a scan. One ScanEvent per scan, stored in the scan event trailer stream at RunHeader.scan_trailer_addr.

The scan event trailer stream begins with a UInt32 count, followed by that many ScanEvent structures.

21.1 Pre-v66 Structure

Order	Type	Field	Description
1	ScanEventPreamble	preamble	Byte array of scan parameters (see §22)
2	UInt32	np	Number of precursor ions (0 for MS1)
3*	Reaction[np]	precursors	Precursor list (only if np > 0)
4	UInt32	unknown_long[1]
5	FractionCollector	fraction_collector	M/z acquisition range
6	UInt32	nparam	Number of conversion coefficients
7*	Float64[nparam]	coefficients	Frequency-to-M/z conversion (see §32)
8	UInt32	unknown_long[2]
9	UInt32	unknown_long[3]

21.2 Version 66 Structure

Version 66 has a significantly restructured ScanEvent layout:

Head:

Order	Type	Field
1	ScanEventPreamble	preamble
2	UInt32	unknown_long[0]
3	UInt32	n_reactions

If dependent scan (n_reactions > 0, i.e. MS2+):

Order	Type	Field
4	Reaction[n_reactions]	precursors
5	Float64	unknown_double[0]
6	Float64	unknown_double[1]
7	UInt32	unknown_long[2]
8	UInt32	unknown_long[3]
9	UInt32	unknown_long[4]
10	FractionCollector	fraction_collector
11	UInt32	nparam
12	Float64[nparam]	coefficients

If primary scan (n_reactions == 0, i.e. MS1):

Order	Type	Field
4	FractionCollector	fraction_collector[0]
5	UInt32	unknown_long[2]
6	UInt32	unknown_long[3]
7	UInt32	unknown_long[4]
8	UInt32	unknown_long[5]
9	FractionCollector	fraction_collector
10	UInt32	unknown_long[6]
11	UInt32	unknown_long[7]
12	UInt32	unknown_long[8]
13	FractionCollector	fraction_collector[2]
14	UInt32	nparam
15	Float64[nparam]	coefficients

Tail (both cases in v66):

Order	Type	Field
last-4	UInt32	unknown_long[a]
last-3	UInt32	unknown_long[b]
last-2	UInt32	unknown_long[c]
last-1	UInt32	unknown_long[d]
last	UInt32	unknown_long[e]

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22. ScanEventPreamble

A byte array encoding the scan type, analyzer, polarity, ionization mode, and other scan parameters. Version-dependent size.

22.1 Common Fields (All Versions, bytes 0-40)

Byte	Field	Values
0	unknown_byte[0]
1	unknown_byte[1]
2	corona	0=Off, 1=On
3	detector	0=Valid, 1=Undefined
4	polarity	0=Negative, 1=Positive, 2=Undefined
5	scan_mode	0=Centroid, 1=Profile, 2=Undefined
6	ms_power	0=Undefined, 1=MS1, 2=MS2, ... 8=MS8
7	scan_type	0=Full, 1=Zoom, 2=SIM, 3=SRM, 4=CRM, 5=Undefined, 6=Q1, 7=Q3
8	unknown_byte[8]
9	unknown_byte[9]
10	dependent	0=Primary (MS1), 1=Dependent (MS2+)
11	ionization	0=EI, 1=CI, 2=FABI, 3=ESI, 4=APCI, 5=NSI, 6=TSI, 7=FDI, 8=MALDI, 9=GDI
12-23	unknown_byte[12-23]
24	activation	1=HCD, 4=CID
25-31	unknown_byte[25-31]
32	wideband	0=Off, 1=On
33-39	unknown_byte[33-39]
40	analyzer	0=ITMS, 1=TQMS, 2=SQMS, 3=TOFMS, 4=FTMS, 5=Sector

22.2 Size by Version

Version	Total Bytes
v8	41
v57, v60	80
v62	120
v63, v64	128
v66	136

22.3 Filter Line Construction

A human-readable filter line can be constructed from the preamble:

{ANALYZER} {POLARITY} {SCAN_MODE} {IONIZATION}{DEPENDENT}{WIDEBAND} {SCAN_TYPE} {MS_POWER} [{LOW_MZ}-{HIGH_MZ}]

Example: FTMS + p NSI Full ms [350.00-1500.00] Example: FTMS + c NSI d Full ms2 542.30@hcd35.00 [100.00-1600.00]

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23. Reaction

Precursor ion information for MS2+ scans. Stored as an array within ScanEvent.

Offset	Size	Type	Field	Description
0x00	8	Float64	precursor_mz	Precursor M/z selected for fragmentation
0x08	8	Float64	unknown_double	Typically 1.0
0x10	8	Float64	energy	Collision/activation energy
0x18	4	UInt32	unknown_long[1]
0x1C	4	UInt32	unknown_long[2]

Total size: 32 bytes

23.1 String Representation

{precursor_mz}@{activation_method}{energy}

Example: 542.30@hcd35.00, 480.25@cid30.00

The activation method name comes from the ScanEventPreamble activation field.

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24. FractionCollector

M/z acquisition range for a scan event.

Offset	Size	Type	Field	Description
0x00	8	Float64	low_mz	Lower M/z bound
0x08	8	Float64	high_mz	Upper M/z bound

Total size: 16 bytes

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