Spectrum Mill - Data Extractor
Spectrum Mill
Peak Picker
Help
Extraction
Maximize CPUs
Remove all prior results
Generate spectral features file only
Show only MS (PMF) parameters
Instrument:
Data Directories
(None Selected)
Files:
*.d *.wiff *.RAW
*.dta *.pkl *.tmp *.mgf
Modifications
Fixed:
MS/MS Spectral Feature Filtering
Precursor MH+
to
Da
Scan time range:
to
min
Disable quality filtering
(Sequence tag length = -1, no merging, attempt to assign charge +1 only)
Sequence tag length >
(For MALDI: Set tag length to -1 and merge secs to total run time.)
Ignore spectra with dissociation mode:
CID
,
ETD
,
PQD
,
HCD
,
EThcD
Merge nearby MS
n
scans with same precursor m/z
Retention time & m/z tolerance: +/-
secs
+/-
m/z
(also used for calculating chromatographic peak area of precursor in MS scans)
(m/z tolerance ignored for high-resolution MS1, dynamically determined based on resolution)
Similarity merging
General MS/MS Merging Constraints:
No merging (tolerate protein quantitation multi-counting)
Retention time & precursor m/z tolerance only
Spectral Similarity & RT & m/z
Precursor Selection Purity & RT & m/z
Precursor Selection Purity & Spectral Similarity & RT & m/z
Specialty MS/MS Merging Options:
Same resolution:
Merge CID & HCD MS
n
Merge CID & PQD MS
n
Different resolution:
Merge ion trap CID & HCD MS
n
immonium ion region
Merge MS
2
and MS
3
spectra from same precursor:
Merge
Merge 5x MS
3
intensity
Create separate extracted files for MS
3
spectra
Ignore MS
3
spectra
Ignore MS
2
spectra
Create additional .mic files (peak detection export)
Agilent ESI TOF data
Min S/N:
Infusion
LC
Time segment for averaging MS scans:
secs
Background subtraction:
Select range
from:
to:
min
Last
min of scan time range
Precursor m/z & Charge Assignment
Centroiding algorithm for profile mode data:
Xcalibur
Spectrum Mill Classic fixed ppm
Precursor Charge:
Default
Find
Force
Force (z):
thru
Maximum (z):
Minimum MS1 S/N:
Find
12
C precursor m/z
MS Noise threshold:
counts (only applies to Agilent Q-TOF)
Results
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