CentralCarbonMetab_Flux_noistd.m
InMemoryMethod
true
false
609
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Auto-generate folder at data file location
true
Report destination
Print
Printer name:
<Default>
Results to include:
HighlightedResults
Maximum number of spectral peaks:
10
1
9223372036854775807
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Limit spectral peaks:
false
Only Visible Columns
true
Show overlaid signals
false
Chromagtogram Anchored Mode
false
Use Blocking Call
true
Report contents
AllDataItems
-1
-1
9223372036854775807
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Selected Template
Single Analysis
Overwrite existing data
false
-1
-1
9223372036854775807
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Column Names
Sorting Column Names
Sorting Order
Delimiter
,
0
0
9223372036854775807
Unspecified
Unspecified
DigitsAfterDecimal
0
None
MaximumCount, SignalToNoiseThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Spectral library path:
Min m/z:
30
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Minimum match score:
50
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Maximum hits per compound:
10
0
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
RTMatchPenalty
Gaussian
Standard deviation
0.1
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Penalty-free RT Range
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
RT range
0.1
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Use RT match (.L, .xml)
false
Limit to the best
true
RT Calibration file:
RT mismatch penalty type
Additive
Max RT penalty:
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
m/z expansion:
SymmetricMz
Single m/z width
0.5
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Single ppm width
100
0.01
1000
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Asymmetric m/z width low
0.3
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Asymmetric m/z width high
0.7
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Adjust score
true
Enable screening
false
Ratio percent uncertainty:
40
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Multi-Library search type:
All
Max m/z:
300
Unspecified
Unspecified
DigitsAfterDecimal
2
None
false
Integrator Selection
Agile
Point sampling:
1
1
9
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Smoothing
false
Filtering:
FivePoint
Start threshold:
0.2
0.001
100
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Stop threshold:
0
0
100
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Peak location:
Top
Baseline reset >
5
0
500
Unspecified
Unspecified
DigitsAfterDecimal
0
None
If either edge <
100
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Preference
Tangent
Tangent skim mode:
Standard
Baseline correction mode:
Classical
Front skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tail skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Skim valley ratio:
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak-to-Valley ratio:
500
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
SlopeSensitivity
False
True
5
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakWidth
False
True
0.05
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
AreaReject
False
True
5
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
HeightReject
False
True
1
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
ShouldersMode
False
True
OFF
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
Shoulder detection
OFF
Threshold:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Area reject:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak width:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
false
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakAreaPctThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Enable system suitability calculations
false
Pharmacopoeia:
USP
Column void time:
0
0
Minutes
Unspecified
DigitsAfterDecimal
1
None
Column length unit:
Centimeters
Column length:
0
0
Centimeters
Unspecified
DigitsAfterDecimal
1
UnitsAndPrecision
Clear previous peak spectra
true
Highlight all peaks
false
Integration
false
false
Integrator Selection
OriginalMsMs
Point sampling:
1
1
9
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Smoothing
false
Filtering:
FivePoint
Start threshold:
0.2
0.001
100
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Stop threshold:
0
0
100
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Peak location:
Top
Baseline reset >
5
0
500
Unspecified
Unspecified
DigitsAfterDecimal
0
None
If either edge <
100
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Preference
Tangent
Tangent skim mode:
Standard
Baseline correction mode:
Classical
Front skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tail skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Skim valley ratio:
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak-to-Valley ratio:
500
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
SlopeSensitivity
False
True
5
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakWidth
False
True
0.05
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
AreaReject
False
True
5
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
HeightReject
False
True
1
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
ShouldersMode
False
True
OFF
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
Shoulder detection
OFF
Threshold:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Area reject:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak width:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
false
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakAreaPctThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Integrator Selection
Agile
Point sampling:
1
1
9
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Smoothing
false
Filtering:
FivePoint
Start threshold:
0.2
0.001
100
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Stop threshold:
0
0
100
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Peak location:
Top
Baseline reset >
5
0
500
Unspecified
Unspecified
DigitsAfterDecimal
0
None
If either edge <
100
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Preference
Tangent
Tangent skim mode:
Standard
Baseline correction mode:
Classical
Front skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tail skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Skim valley ratio:
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak-to-Valley ratio:
500
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
SlopeSensitivity
False
True
5
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakWidth
False
True
0.05
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
AreaReject
False
True
5
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
HeightReject
False
True
1
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
ShouldersMode
False
True
OFF
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakAreaPctThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Shoulder detection
OFF
Threshold:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Area reject:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak width:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
false
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
Enable system suitability calculations
false
Pharmacopoeia:
USP
Column void time:
0
0
Minutes
Unspecified
DigitsAfterDecimal
1
None
Column length unit:
Centimeters
Column length:
0
0
Centimeters
Unspecified
DigitsAfterDecimal
1
UnitsAndPrecision
Integrator Selection
Agile
Point sampling:
1
1
9
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Smoothing
false
Filtering:
FivePoint
Start threshold:
0.2
0.001
100
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Stop threshold:
0
0
100
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Peak location:
Top
Baseline reset >
5
0
500
Unspecified
Unspecified
DigitsAfterDecimal
0
None
If either edge <
100
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Preference
Tangent
Tangent skim mode:
Standard
Baseline correction mode:
Classical
Front skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tail skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Skim valley ratio:
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak-to-Valley ratio:
500
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
SlopeSensitivity
False
True
5
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakWidth
False
True
0.05
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
AreaReject
False
True
5
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
HeightReject
False
True
1
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
ShouldersMode
False
True
OFF
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
Shoulder detection
OFF
Threshold:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Area reject:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak width:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
false
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakAreaPctThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Smoothing function:
Gaussian
Function width:
15
ScanNumber
ScanNumber
DigitsAfterDecimal
0
None
Gaussian width:
5
0
Minutes
AcqTime
DigitsAfterDecimal
3
None
Exclude masses:
false
Excluded m/z:
Thompsons
MassToCharge
DigitsAfterDecimal
4
Thompsons
MassToCharge
DigitsAfterDecimal
4
0
0
PrecisionOnly
PSetExcludeMassSingleMzExpansionMode
SymmetricMz
Width (m/z):
0.5
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Width (ppm):
100
10
1000
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Low width (m/z):
0.3
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
High width (m/z):
0.7
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Automatically compute when chromatograms are integrated
false
Signal definition:
Height
Noise definition:
PeakToPeak
1
1
9
Unspecified
Unspecified
DigitsAfterDecimal
1
None
true
Noise regions:
Minutes
AcqTime
DigitsAfterDecimal
3
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Desired length:
1
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Minimum length:
0.1
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Start time:
0
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
End time:
10
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Noise region width:
0.25
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
1
Quadrupole
1
0
0
False
Quadrupole
1
0
0
False
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Baseline Chunk Size
4
4
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Minimum Chunks
10
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Fraction Skip
0.02
0.01
0.999
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Baseline Fraction Use
0.05
0.01
0.999
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Tolerance
0.25
0.05
5000
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Detect Maximum Spike Width
2
0
10
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Detect Required Valley
0.7
0
1
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Restrict X-Range
false
X-Range
0
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
0
20000
0
20000
PrecisionOnly
Fast Baseline
true
MaximumCount
Peak height (counts) >=
100
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to the largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
5
0
Mixed
Mixed
DigitsAfterDecimal
1
None
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
true
true
true
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
false
false
Isotope spacing tolerance(m/z)
0.0025
0
0.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
None
Isotope spacing tolerance(ppm)
7
0
200
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Remove higher isotopes
false
Recompute when peak list changes
true
Maximum charge state
2
1
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum charge state
0
0
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Limit assigned charge states to a maximum of:
true
Isotope model
CommonOrganicMolecules
Treat ions with unassigned charge as singly-charged
false
Sum abundance
true
Baseline Chunk Size
4
4
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Minimum Chunks
10
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Fraction Skip
0.02
0.01
0.999
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Baseline Fraction Use
0.05
0.01
0.999
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Tolerance
0.25
0.05
5000
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Detect Maximum Spike Width
2
0
10
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Detect Required Valley
0.7
0
1
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Restrict X-Range
false
X-Range
0
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
0
20000
0
20000
PrecisionOnly
Fast Baseline
true
MaximumCount
Peak height (counts) >=
10
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to the largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
5
0
Mixed
Mixed
DigitsAfterDecimal
1
None
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
true
true
true
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
false
false
Isotope spacing tolerance(m/z)
0.0025
0
0.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
None
Isotope spacing tolerance(ppm)
7
0
200
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Remove higher isotopes
false
Recompute when peak list changes
true
Maximum charge state
2
1
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum charge state
0
0
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Limit assigned charge states to a maximum of:
true
Isotope model
CommonOrganicMolecules
Treat ions with unassigned charge as singly-charged
false
Sum abundance
true
Retention time window:
0.25
0
2
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Positive MS/MS TIC threshold:
1000
0
Abundance
Response
DigitsAfterDecimal
0
None
Negative MS/MS TIC threshold:
1000
0
Abundance
Response
DigitsAfterDecimal
0
None
Mass match tolerance:
0.05
0.001
1
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Limit to the largest compounds:
false
Maximum number of compounds:
50
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Omit persistent background compounds >
5
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Extract ECC:
true
Extract EIC:
true
EIC single m/z expansion:
75
50
Thompsons
MassToCharge
DigitsAfterDecimal
3
None
0.5
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
true
Extract MS:
true
Extract MS:
false
MS background subtraction:
None
Except when the TIC >
100000
0
100000
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Filter results by fragments
false
Fragment mass:
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Neutral loss:
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Mass filter
FragmentMass
Width (m/z):
0.5
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Width (ppm):
100
10
1000
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Low width (m/z):
0.3
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
High width (m/z):
0.7
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Single m/z expansion:
SymmetricMz
Match all the specified fragments
false
Delete previous compounds
true
Highlight all compounds
false
FindCompounds
false
false
Maximum chromatogram peak width
0.25
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Limit to the largest compounds:
false
Maximum number of compounds:
50
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Generate library spectra
false
MaximumCount, PeakAreaPctThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
10
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Restrict retention times:
false
Retention time range:
0
0
PrecisionOnly
Restrict m/z range:
false
m/z range:
0
0
PrecisionOnly
PeakHeightAbsThreshold
Use peaks with SNR >=
5
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Use peaks with height >=
100
0
Abundance
Response
DigitsAfterDecimal
0
None
Positive ions:
true
1
-1
1
H
true
1
-1
1
Na
true
1
-1
1
K
true
1
-1
1
NH4
true
1
-1
1
H
true
1
-1
1
Na
true
1
-1
1
K
true
1
-1
1
NH4
Negative ions:
true
1
1
-1
H
true
1
1
1
Cl
false
1
1
1
Br
false
1
1
1
HCOO
false
1
1
1
CH3COO
false
1
1
1
CF3COO
true
1
1
-1
H
true
1
1
1
Cl
false
1
1
1
Br
false
1
1
1
HCOO
false
1
1
1
CH3COO
false
1
1
1
CF3COO
Salt dominated positive ions:
false
Maximum charge state to assign
4
1
10
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Assume peptidic isotope distribution:
false
Maximum peaks per spectrum
500
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Background
None
Assume unidentified ions are radical ions
false
Target data type
SmallMolecules
Neutral Species Definitions
false
1
0
0
H2O
false
1
0
0
H3PO4
false
1
0
0
H2O
false
1
0
0
H3PO4
Clip extracted raw spectrum:
false
Single Mz Expansion Mode
AsymmetricMz
SingleMzWidth
10
1
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
SingleMzWidth
5
1
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
AsymWidthHigh
10
1
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Typical RT peak width
false
min
0.2
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Smoothing
true
times peak width
0.2
0
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Smoothing
true
length
50
0
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Remove spikes
false
max spike width
0.25
0
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Smooth peaks
true
times peak width
1
0
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Remove wide peaks
false
min peak width
10
0
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Display only the largest
false
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Prefer profile for raw spectra, if available
false
Extract MS/MS Spectrum
false
Average MSMSSpectrum per CE
false
Single m\z Expansion mode
AsymmetricMz
Tolerance
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tolerance
0.05
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tolerance Unit
ITEM_PPM
Deisotope MS/MS spectrum
true
Restrict RTspan of EIC
true
Minimum RT span (minutes)
2
1
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Desired RTspan (+/- Width * this)
10
1
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Abundance filter type
PeakHeightAbsThreshold, PeakHeightPctThreshold
Peak height (%) >=
2.5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
5000
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Maximum number of compounds:
100
1
2147483647
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Restrict retention times:
false
Retention time:
Minutes
AcqTime
DigitsAfterDecimal
3
Minutes
AcqTime
DigitsAfterDecimal
3
0
0
PrecisionOnly
Restrict charge states:
false
Charge states:
1
10
1
10
None
Restrict to neutral losses:
false
Neutral loss mass:
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Compounds without isotopes
Include
Compounds without masses
Exclude
Filter mass list
false
Mass(es) to include/exclude
Daltons
Mass
DigitsAfterDecimal
4
Daltons
Mass
DigitsAfterDecimal
4
0
0
PrecisionOnly
5
0
1000
PartsPerMillion
Mass
DigitsAfterDecimal
3
None
Filter optionis for mass(es)
Include
Database
false
Quality score
80
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Filter results on mass defects
false
Expected defect is constant:
true
Expected defect:
0
-10.5
10.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Defect slope:
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Defect slope denominator:
100
1
1000
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tolerance type:
ConstantSymmetric
Tolerance:
0.01
0
0.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Tolerance (negative);
0.01
0
0.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Tolerance slope:
0
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Tolerance slope denominator:
100
1
1000
Unspecified
Unspecified
DigitsAfterDecimal
2
None
true
true
true
Delete previous compounds
true
Highlight all compounds
false
FindCompounds
false
false
Database Path
C:\MassHunter\PCDL\default.csv
Group transitions by compound name
true
Detect most abundant peak by peak area
true
Integrator Selection
Agile
Point sampling:
1
1
9
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Smoothing
false
Filtering:
FivePoint
Start threshold:
0.2
0.001
100
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Stop threshold:
0
0
100
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Peak location:
Top
Baseline reset >
5
0
500
Unspecified
Unspecified
DigitsAfterDecimal
0
None
If either edge <
100
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Baseline Preference
Tangent
Tangent skim mode:
Standard
Baseline correction mode:
Classical
Front skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tail skim height ratio:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Skim valley ratio:
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak-to-Valley ratio:
500
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
SlopeSensitivity
False
True
5
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakWidth
False
True
0.05
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
AreaReject
False
True
5
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
HeightReject
False
True
1
-1.79769313486232E+308
Unspecified
Unspecified
DigitsAfterDecimal
2
None
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
ShouldersMode
False
True
OFF
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
Shoulder detection
OFF
Threshold:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Area reject:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Peak width:
0
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
false
BaselineNow
True
True
true
BaselineNow
False
True
true
0
0
Minutes
Unspecified
DigitsAfterDecimal
3
PrecisionOnly
PeakAreaPctThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Whole spectrum using library search
false
Generate formula for each peak if no library hit found
false
Identify individual peaks in spectrum
true
No identification
false
Maximum number of peaks to identify (per spectrum)
5
1
5000
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Search a database for each peak
false
Generate formula for each peak
false
Generate formulas for peaks with no database hits
true
Chromatogram used to find mass spectra
TotalIon
Get Signal A from
DiodeArrayDetector
Get Signal A from
CE1
1
1
9
Unspecified
Unspecified
DigitsAfterDecimal
0
None
BPC m/z range:
Thompsons
MassToCharge
DigitsAfterDecimal
4
Thompsons
MassToCharge
DigitsAfterDecimal
4
0
0
PrecisionOnly
Search Fields
Mass
Use Absolute Mass Tolerance
false
Absolute Mass Tolerance
5
0
1000
MilliThompsons
MzDifference
DigitsAfterDecimal
2
None
Relative Mass Tolerance
5
0
1000
PartsPerMillion
RelativeDifference
DigitsAfterDecimal
2
None
Retention Time Tolerance
0.1
0
1000
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Limit to the best
true
Maximum Hits
10
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Consider isotope abundance ratios when ranking hits
false
Maximum number of peaks to search when peaks are not specified graphically:
5
1
10
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Search "neutral" database entries for masses from simple ions
false
Database Path
C:\MassHunter\PCDL\default.csv
Positive ions:
false
1
-1
0
true
1
-1
1
H
true
1
-1
1
Na
false
1
-1
1
K
false
1
-1
1
NH4
false
1
-1
0
true
1
-1
1
H
true
1
-1
1
Na
false
1
-1
1
K
false
1
-1
1
NH4
Positive Neutral Loss:
false
1
0
0
H2O
false
1
0
0
H2O
Positive Charge State Range
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
1
10
1
10
None
Positive Dimer
false
Positive Trimer
false
Negative ions:
false
1
1
0
true
1
1
-1
H
false
1
1
1
Cl
false
1
1
1
Br
true
1
1
1
HCOO
true
1
1
1
CH3COO
false
1
1
1
CF3COO
false
1
1
0
true
1
1
-1
H
false
1
1
1
Cl
false
1
1
1
Br
true
1
1
1
HCOO
true
1
1
1
CH3COO
false
1
1
1
CF3COO
Negative Neutral Loss:
false
1
0
0
H2O
false
1
0
0
H2O
Negative Charge State Range
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
1
10
1
10
None
Negative Dimer
false
Negative Trimer
false
Spectral library path:
Limit to the best
false
Maximum hits per compound:
10
0
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Search criteria
CollisionEnergy, FragmentationVoltage, Polarity, ScanType, InstrumentType, PrecursorIon
Search method
Reverse
2
0
Volts
Voltage
DigitsAfterDecimal
2
PrecisionOnly
Precursor Ion m/z ppm
10
0
1000
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Precursor Ion m/z mDa
2
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Product ion m/z ppm
20
0
1000
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Product ion m/z mDa
2
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Minimum forward match score:
25
0
100
Unspecified
MatchScore
DigitsAfterDecimal
2
None
Minimum reverse match score:
80
0
100
Unspecified
MatchScore
DigitsAfterDecimal
2
None
Exclude precursor ion from reverse score
true
Percentage of total MS/MS intensity that precursor ion must exceed to be excluded from reverse score
90
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Spectral library path:
Apply to search database path
false
false
PeakHeightAbsThreshold, PeakHeightPctThreshold
Peak height (counts) >=
100
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
0.5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to the largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
5
0
Mixed
Mixed
DigitsAfterDecimal
1
None
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
true
true
true
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
false
false
61.064791
2
10000
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
1
-100
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
MS nitrogen rule:
EvenElectron
Positive ions:
H
Negative ions:
H
Element Limits
C
3
60
H
0
120
O
0
30
N
0
30
S
0
5
Cl
0
3
C
3
60
H
0
120
O
0
30
N
0
30
S
0
5
Cl
0
3
Maximum neutral mass for which formulas should be calculated:
750
100
5000
Daltons
Mass
DigitsAfterDecimal
4
PrecisionOnly
Max. mass error:
7.5
0
1000
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
m/z error units:
PartsPerMillion
Minimum score
35
0
100
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Minimum overall score per charge carrier
true
Maximum MS mass error
false
Require DBE from
false
0
-0.5
99
Unspecified
Unspecified
DigitsAfterDecimal
1
None
50
-0.5
99
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Maximum number of hits per charge carrier
false
Maximum number of hits per charge carrier
5
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
MS Mass Coeff (MDa)
2
0
100
MilliDaltons
Mass
DigitsAfterDecimal
1
None
MS Mass Coeff (Ppm)
5.6
0
100
PartsPerMillion
Mass
DigitsAfterDecimal
1
None
MS MS Mass Coeff (MDa)
2.5
0
100
MilliDaltons
Mass
DigitsAfterDecimal
1
None
MS MS Mass Coeff (Ppm)
7.5
0
100
PartsPerMillion
Mass
DigitsAfterDecimal
1
None
MS isotope abundance
7.5
0
100
Percent
RelativeDifference
DigitsAfterDecimal
1
None
Formula generation rules
B0201
Include target formula in results
false
Target formula
Positive ions:
false
1
-1
0
true
1
-1
1
H
false
1
-1
1
Na
false
1
-1
1
K
false
1
-1
1
NH4
false
1
-1
1
C2H5
false
1
-1
1
C3H5
false
1
-1
1
C4H9
false
1
-1
0
true
1
-1
1
H
false
1
-1
1
Na
false
1
-1
1
K
false
1
-1
1
NH4
false
1
-1
1
C2H5
false
1
-1
1
C3H5
false
1
-1
1
C4H9
Negative ions:
false
1
1
0
true
1
1
-1
H
false
1
1
1
Cl
false
1
1
1
Br
false
1
1
1
COOH
false
1
1
1
CF3COO
false
1
1
1
CH3COOH
false
1
1
0
true
1
1
-1
H
false
1
1
1
Cl
false
1
1
1
Br
false
1
1
1
COOH
false
1
1
1
CF3COO
false
1
1
1
CH3COOH
Group hits with same formula (but different charge carriers)
true
MaximumCount, PeakHeightAbsThreshold, PeakHeightPctThreshold
Peak height (counts) >=
10
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
0.1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to the largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
5
0
Mixed
Mixed
DigitsAfterDecimal
1
None
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
true
true
true
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
false
true
MS mass coeff (mDa)
2
0
100
MilliDaltons
Mass
DigitsAfterDecimal
1
None
MS mass coeff (ppm)
5.6
0
100
PartsPerMillion
RelativeDifference
DigitsAfterDecimal
1
None
MS/MS mass coeff (MDa)
5
0
100
MilliDaltons
Mass
DigitsAfterDecimal
1
None
MS/MS mass coeff (ppm)
7.5
0
100
PartsPerMillion
RelativeDifference
DigitsAfterDecimal
1
None
MS isosope abundance
7.5
0
100
Percent
RelativeDifference
DigitsAfterDecimal
1
None
Retention time:
0.115
0
10
Unspecified
Unspecified
DigitsAfterDecimal
3
None
Isotope abundance score
60
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Mass score
100
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Isotope spacing score
50
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Retention time score
100
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
MS/MS score weight
50
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
PeakHeightAbsThreshold, PeakHeightPctThreshold
Peak height (counts) >=
100
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
0.1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to the largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
5
0
Mixed
Mixed
DigitsAfterDecimal
1
None
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
true
true
true
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
false
false
Positive ions:
+H
Negative ions:
-H
Isotope spacing tolerance(m/z)
0.0025
0
0.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
None
Isotope spacing tolerance(ppm)
7
0
200
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Remove higher isotopes
false
Recompute when peak list changes
true
Maximum charge state
2
1
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum charge state
0
0
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Limit assigned charge states to a maximum of:
true
Isotope model
Peptides
Treat ions with unassigned charge as singly-charged
true
Sum abundance
true
Show user chromatograms
true
With peak tables
true
With signal to noise results
false
Show user spectra
true
Show library spectrum
false
Show difference spectrum
false
With peak tables
true
Show compound chromatograms
true
With peak tables
false
Show compound spectra
true
With peak tables
true
Show compound table
true
Sort compound table in increasing order:
true
Show user chromatogram(s)
false
Show compound chromatogram(s)
true
Overlay compound chromatogram(s)
false
Show MS spectrum
true
Show library spectrum
false
Show difference spectrum
false
Show MS peak table
true
Show predicted isotope match table
false
Show MS spectrum (zoomed in on special peaks)
true
Overlay predicted isotope distribution
true
Show MS/MS spectrum
true
Show MS/MS peak table
true
Left zoom limit
30
0
1.79769313486232E+308
Thompsons
MassToCharge
DigitsAfterDecimal
1
None
Right zoom limit
30
0
1.79769313486232E+308
Thompsons
MassToCharge
DigitsAfterDecimal
1
None
Sort compound table by
RetentionTime
Exclude details for unidentified compounds
false
Template Folder
C:\MassHunter\Report Templates\Qual\B.07.00\en-US\Letter
Analysis report template :
AnalysisReport
Compound report template :
CompoundReport
Plot window report template :
Graphic
RawData
Table window report template :
Table
MS Tune report template :
MS Tune
Qualitative method report template :
QualitativeMethodReport
Acquisition method report template :
AcqMethodReport
Page orientation
Portrait
Chromatogram peaks
true
Max Chrom Peaks
10
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Mass spectrum peaks
true
Max Spectrum Peaks
10
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Hide empty columns in tables
true
Show sample information
true
User chromatograms
false
Compound chromatograms
false
MS spectra
false
MS/MS spectra
false
Deconvoluted spectra
false
UV spectra
false
User chromatograms
2
10
Minutes
AcqTime
DigitsAfterDecimal
3
0
999
0
999
PrecisionOnly
Compound chromatograms
0
999
0
999
PrecisionOnly
MS spectra
100
1200
Thompsons
MassToCharge
DigitsAfterDecimal
4
0
20000
0
20000
PrecisionOnly
MS/MS spectra
0
20000
0
20000
PrecisionOnly
Deconvoluted spectra
15000
35000
Daltons
DeconvolutedMass
DigitsAfterDecimal
2
0
750000
0
750000
PrecisionOnly
UV spectra
240
330
Nanometers
Wavelength
DigitsAfterDecimal
0
190
1000
190
1000
PrecisionOnly
Limit identification hits
true
10
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Content to include
AllResults
Print report
true
Printer name
<Default>
Print preview
false
Save report as Excel file
false
Save report as PDF file
false
Separate report per data file
true
Inside data file's reports subdirectory
true
At specified directory
C:\MassHunter\reports
Overwrite existing report
false
User
true
Export to the batch location
false
One export file per data file
true
At the location of the data file
true
Specified export directory
C:\MassHunter\Data
Specified export file name
c:\temp\exportFile
Overwrite existing export file
false
Peak window:
0.04
0
Minutes
Unspecified
DigitsAfterDecimal
2
None
Export entire data file
true
Export only highlighted
false
MS level type
All
MS storage mode to use
PeakDetectedSpectrum
Compute deisotope
false
PeakHeightAbsThreshold, PeakHeightPctThreshold
Peak height (counts) >=
10
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
0.1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to the largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
5
0
Mixed
Mixed
DigitsAfterDecimal
1
None
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
true
true
true
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
false
false
Isotope spacing tolerance(m/z)
0.0025
0
0.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
None
Isotope spacing tolerance(ppm)
7
0
200
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Remove higher isotopes
false
Recompute when peak list changes
true
Maximum charge state
2
1
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum charge state
0
0
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Limit assigned charge states to a maximum of:
true
Isotope model
CommonOrganicMolecules
Treat ions with unassigned charge as singly-charged
false
Sum abundance
true
PeakHeightAbsThreshold, PeakHeightPctThreshold
Peak height (counts) >=
10
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
0.1
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to the largest:
100
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
5
0
Mixed
Mixed
DigitsAfterDecimal
1
None
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
true
true
true
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
false
false
Isotope spacing tolerance(m/z)
0.0025
0
0.5
Thompsons
MassToCharge
DigitsAfterDecimal
4
None
Isotope spacing tolerance(ppm)
7
0
200
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Remove higher isotopes
false
Recompute when peak list changes
true
Maximum charge state
2
1
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum charge state
0
0
99
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Limit assigned charge states to a maximum of:
true
Isotope model
CommonOrganicMolecules
Treat ions with unassigned charge as singly-charged
false
Sum abundance
true
Retention time window:
0
-100
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Retention time window:
0.25
0
1
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Limit number of precursor ions per compound to
1
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Limit number of precursor ions per compound to
true
PSetExportInclusionList_MinimunIonAbundance
2000
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum ion abundance:
true
Export monoisotopic m/z
true
Specify charge state preference order
false
Method path:
C:\MassHunter
Only highlighted compounds
false
PSetExportInclusionList_SelectedChargeStates
2
3
>3
2
3
>3
false
1
-1
0
true
1
-1
1
H
false
1
-1
1
Na
false
1
-1
1
K
false
1
-1
1
NH4
false
1
-1
0
true
1
-1
1
H
false
1
-1
1
Na
false
1
-1
1
K
false
1
-1
1
NH4
false
1
1
0
true
1
1
-1
H
false
1
1
1
Cl
false
1
1
1
Br
false
1
1
1
HCOO
false
1
1
1
CH3COO
false
1
1
1
CF3COO
false
1
1
0
true
1
1
-1
H
false
1
1
1
Cl
false
1
1
1
Br
false
1
1
1
HCOO
false
1
1
1
CH3COO
false
1
1
1
CF3COO
ChargeStatePriorities
ChargeState
1
Priority
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
ChargeState
2
Priority
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
ChargeState
3
Priority
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
ChargeState
>3
Priority
2
Unspecified
Unspecified
DigitsAfterDecimal
0
None
ChargeState
Unknown
Priority
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Sort exclusion list by:
RetentionTime
Export inclusion list format
AutoMsMsPreferred
Sort Ascending
true
script1
Save Complete Results
false
script1
script2
script3
Limit operations to specific retention times:
false
Limit operations to:
Minutes
AcqTime
DigitsAfterDecimal
3
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Delete all previous results
true
Highlight all compounds
false
FindCompounds
true
false
Compound mining algorithm
FindByMolecularFeature
Search a database for each compound
false
Generate formulas for each compound
false
Generate formulas for peaks with no database hits
true
Chromatogram Polarity:
Mixed
Signal device Type
DiodeArrayDetector
m/z range:
Thompsons
MassToCharge
DigitsAfterDecimal
4
Thompsons
MassToCharge
DigitsAfterDecimal
4
0
0
PrecisionOnly
Match sequences for each compound
false
Show only identified compounds
true
Search a library for each compound
false
Do sample purity calculations
false
Compound EIC
false
Compound spectrum
false
Formula source to confirm
Worklist
Specified formulas
Use Absolute Mass Tolerance
false
Retention Time Tolerance
0.35
0
1000
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Single Mz expansion mode:
SymmetricPpm
Asymmetric low
0.1
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Asymmetric high
0.15
0
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Single m/z width:
0.5
0
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Asymmetric Mz width low:
0.3
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Asymmetric Mz width high:
0.7
0
10
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Absolute Mass Tolerance
5
0
1000
MilliThompsons
MzDifference
DigitsAfterDecimal
2
None
Expected retention time
1
0
Minutes
AcqTime
DigitsAfterDecimal
2
None
Search Fields
Mass, OptionalRetentionTime
Relative Mass Tolerance
10
0
1000
PartsPerMillion
RelativeDifference
DigitsAfterDecimal
2
None
Single ppm width:
35
10
1000
Unspecified
Unspecified
DigitsAfterDecimal
1
None
Polarity:
Mixed
Only generate compounds for matched formulas
false
Max hits per formula:
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum abundance:
10
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Minimum cluster coverage for EIC:
75
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Maximum cluster ions for EIC:
5
1
20
Unspecified
Unspecified
DigitsAfterDecimal
0
None
CefPath
Automatically increase for isomeric compounds
true
Do not match if score is
true
Reject score threshold
70
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Do not match if the (unobserved) second ion’s abundance is expected to be
true
Reject second ion threshold
200
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Prefer profile for raw spectra, if available
true
Clip extracted raw spectra
true
Asymmetric low width
5
1
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Asymmetric high width
10
1
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Single width
5
1
Thompsons
MassToCharge
DigitsAfterDecimal
4
PrecisionOnly
Average MS/MS spectrum for all CE's
false
Precursor tolerance
20
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Precursor tolerance
0.05
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Tolerance unit
ITEM_PPM
Deisotope MS/MS spectrum
true
Include structure
false
Warn if score is
true
Warn if the (unobserved) second ion’s abundance is expected to be
true
Warn score threshold
75
0
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Warn single ion threshold
50
0
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Smooth EIC before integration
false
LOW energy channel spectra with
ALLIONS_OR_CLASSIC
Confirm with fragment ions
false
Molecular ion optional
false
Coelution score
90
0
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Use spectral library only
true
Number of most specific ions from spectral library
5
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Number of most specific ions from average fragment spectrum
7
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
RT difference
0.1
0
1
Unspecified
Unspecified
DigitsAfterDecimal
2
None
S/N ratio
true
5
2
100
Unspecified
Unspecified
DigitsAfterDecimal
2
None
Minimum number of qualified fragments
true
1
1
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
Minimum percent of qualified fragments
75
0
100
Unspecified
Unspecified
DigitsAfterDecimal
0
None
MaximumCount, PeakAreaAbsThreshold
Peak area (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak area (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Peak height (counts) >=
10000
0
Abundance
Response
DigitsAfterDecimal
0
None
Peak height (%) >=
5
0
100
Abundance
Response
DigitsAfterDecimal
3
None
Limit to largest:
5
0
Unspecified
Unspecified
DigitsAfterDecimal
0
None
0
0
Abundance
Response
DigitsAfterDecimal
2
None
30
0
Unspecified
Unspecified
DigitsAfterDecimal
1
None
1
1
Unspecified
Unspecified
DigitsAfterDecimal
0
None
false
Annotate fragment spectrum peaks with formulas
false
Generate formulas for non-fragment (unknown) ions
false
true
true
false
Compute sample purity
false
Algorithm to use
TIC
Use peak areas
true
RT acceptance window: +/-
0.05
0
0.5
Minutes
AcqTime
DigitsAfterDecimal
3
PrecisionOnly
Single algorithm
true
TIC
Minimum of all selected algorithms
false
Average of all selected algorithms
false
Maximum of all selected algorithms
false
Minimum acceptable purity
75
0
100
Percent
Unspecified
DigitsAfterDecimal
0
None
Matching Source
SequenceMass
Sequences
true
Mass(es)
false
Masses:
0
750000
Daltons
Mass
DigitsAfterDecimal
3
None
MS mass coeff (mDa)
2
0
100
MilliDaltons
Mass
DigitsAfterDecimal
1
None
MS mass coeff (ppm)
5.6
0
100
PartsPerMillion
Mass
DigitsAfterDecimal
1
None
MS/MS mass coeff (MDa)
5
0
100
MilliDaltons
Mass
DigitsAfterDecimal
1
None
MS/MS mass coeff (ppm)
7.5
0
100
PartsPerMillion
Mass
DigitsAfterDecimal
1
None