Agilent 1100 Series LC/MSD Trap System Quick Start Guide 5
Trap control/data acquisition
• New isolation parameters
• New fragmentation parameters to eliminate isotopic discrimination effects
• New "Standby" mode (orange) to allow shutdown of the MSD Trap Control
software while maintaining MS in “Standby” state
DataAnalysis
Data files
acquired with the
5.2 software
cannot be
processed using
previous versions
of the software.
• Alternating polarity analyses to find compounds with spectra of both polarities.
Applies to Find Compounds - AutoMS(n), - Chromatogram, - Dissect.
• Subtraction of 2D spectral background to view chromatograms and spectra and
to calculate compound mass spectra.
• Charge deconvolution on line spectra and export of results to XML and MGF
• Time range argument for Find Compounds - AutoMS(n) and Find Compounds -
Dissect automation commands
• Ability to exclude MS/MS spectra for Find compounds - AutoMS(n) if they do
not exhibit characteristic mass differences (e.g., for amino acids)
• Improved Neutral Loss Chromatogram (capability to specify multiple losses;
also available with automation)
• Creation of “pseudo” Neutral Loss Spectra, where all mass signals in a MS/MS
spectrum are labeled as mass differences relative to the precursor ion
• Improved handling of Agilent data file format export (scaling, option to export
line or profile data in manual and automatic fashion)
• Manual deconvolution with Charge State Ruler
• Compound List Filter to enable/disable compounds based on Library Search or
Intensity Criteria
• Building Block Editor for automatic annotation of amino acids and nucleic
acids via ‘Difference Ruler’
• Improved Find Compounds - AutoMS(n) algorithm (limits algorithm to find the
x most intense compounds)
• Improved monoisotopic peak determination of precursor
• Library Search: Inclusion of the measured mass range with the spectrum
properties.
QuantAnalysis
• Improved weighted calibration
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