ACD/MS Manager

What's New

Version 9.0 to 10.0

Improved Fragment Assignment

• Neutral loss reactions added to the fragmentation rule set
• Additional ionization and fragmentation reactions have been added to the fragmentation rule set

Enhancements to Formula Generator

• Ionization parameters added to Formula Generator; output the formula for the neutral or charged form
• Generate the neutral formula from adduct ion peaks in the mass spectrum

Advancements to LC/UV (DAD, PDA) data processing

• Peak picking for LC/UV datasets
• Baseline correction for LC/UV datasets allows you to subtract the solvent background, and extract accurate UV-Vis spectra for chromatographic peaks
• Easier transfer of peak information (e.g., label, chemical structure) with the manual peak matching tool

New Chromatographic Data Support Features

• Automatic import of chromatographic parameters for MassLynx and Agilent LC/MS data Chromatographic parameters are stored in the new HPLC Parameters form, which may also be manually updated
• Export the TIC, now along with peak labels, retention times, and structures to ChromManager
• Select and label individual mass chromatogram peaks, which are now added to the Table of Peaks for the whole dataset
• Manually edit peak names in the Table of Peaks

Updates to Supported File Types:

• Improved JCAMP file support now allows import of ionization information
• Improved import of previously processed Waters MassLynx data
• New *.Wiff data import filter added to the MS File Splitter/Conversion utility
• Support for Waters Millennium LC/MS files
• Support for uniquely named Agilent and Bruker *.yep files (i.e., other names than Analysis.yep)
• Support for Thermo Xcalibur version 2.0
• Support for Waters MassLynx version 4.1
• Enhanced support of AB MDS Sciex Analyst 4.1.1 files

Other New Features

• Convert profile data to centroid data for LC/MS datasets, and single mass spectra. This is also available for macro automation
• Improved mass chromatogram display
• Save and load Ion Presence labeling lists

Version 8.0 to 9.0

Improved Fragment Assignment:

• Assign ion clusters, including different isotopes of the same fragment.
• Evaluate the quality of the fragment assignment using the Assignment Quality Index (AQI).
• Improved N-oxide fragmentation scheme.

Enhancements to Mass Chromatogram Display and Processing:

• Increased speed of processing and display of mass chromatograms.
• Additional peak picking options:
  • Threshold area value.
  • m/z range.
• Mass chromatogram smoothing options:
  • Apply FFT or Savitzky-Golay smoothing functions.
• Identify and label relevant mass chromatogram peaks with ACD/Ion Presence™:
  • Find and label mass chromatogram peaks with a specific mass or mass difference from a reference mass.

Compare Mass Spectra Using Advanced Spectral Subtraction Options and Spectral Mirroring:

• Expanded spectral subtraction options:
  • Apply m/z based, intensity based, or interpolation subtraction to subtract the relative intensities of ions between spectra.
  • Use Boolean subtraction to remove common peaks between spectra.
  • Remove the major peaks within a spectrum using single peak subtraction.
• Spectral Mirroring:
  • Display two mass spectra using a common x-axis. One is displayed above the axis, and the other is displayed below.

New Database Features:

• Link an MS/MS spectrum to the parent ion in the corresponding MS spectrum.
• Unify legacy data from different instrument vendors with User Data Mapping.

Updates to Supported File Types:

• New file formats supported by ACD/MS Manager are:
  • Import LC/MS data from Agilent LC TOF wiff files.
  • Import LC(GC)/MS data from JEOL K9 files.
  • Import a single spectrum or LC(GC)/MS data files from MasCom MASPECII³² files.
  • Import or export LC(GC)/MS data in MATLAB/Eigenvector DSO format.
  • Import DAD data from MDS SCIEX Analyst (any data type now supported).

Other New Features:

• Ease-of-Use Features:
  • Select from pre-set relative chromatogram and mass spectrum window pane sizes.
  • Easier creation of averaged and combined spectra.
  • Table of Mass Chromatograms can now be sorted using any number of columns.
• Attach a mass value to a Markush structure.

Version 7.0 to 8.0

I) Enhanced Import data support:

• Support additional data import formats:
  • Import LC/MS data from Mariner ASCII (*.txt) data files
  • Import Varian 1200 (*.dat) data files
  • Import LC/MS Shimadzu LCMSsolution (*.qld) data files
  • Import the Bruker (*.yep) data files produced by Bruker Esquire LC/MS Ion Trap and Agilent LC/MSD Trap instruments
  • Import profile, GC/MS, and LC/MS data in Thermo Galactic (*.spc) format
• Monitor file import progress with the File Import Progress Indicator bar
• Import data using the enhanced and redesigned Import dialog box with spectral preview, new shortcut and navigation options

II) Import vendor files with greater ease using Import dialog boxes that are tailored to vendor-specific conventions and approaches:

• Select Thermo Electron Xcalibur® channels to be imported in an improved Data Import dialog box
• Sort the import dialog box by any desired field for MDS SCIEX Analyst wiff and PE SCIEX API to Piff
• Store automatically the Waters MassLynx™ *.inf and *.txt file information, instrument tuning parameters, and Sample ID in the ACD/Labs data file
• Autoname imported data descriptively according to the selected experiment types and vendor specific parameters in an ACD/Labs format electronic file. The name appears on the toolbar and as the proper name of the electronic file when saved

III) Data Export to other modules for advanced processing has been enhanced:

• Use the enhanced Export to ACD/UV-IR Manager command
• Create a report on the fly by copying a chromatogram to the Clipboard and pasting it to your report application

IV) Mass Chromatogram display and analysis tools have been enhanced (more details):

• Review Mass Chromatogram at any time from the main interface
• Review mass chromatogram data faster with the improved Table of Mass Chromatograms
  • Sort priority can be set across three columns to better organize table data
• Manually extract mass chromatograms from within the CODA or COMPARELCMS modes
• The mass chromatograms are color coded with an enhanced color pallet with 150 distinctive colors
  • All mass chromatograms with the same mass value share the same color
• Normalize the extracted mass chromatogram display to the maximum of each trace to better confirm the presence of closely co-eluting components
• Set the option to "Hide MC Curves Without Peaks Found" in the shortcut window

V) Analysis capability enhancement were added to help extract the data you need

• Define a Relative Retention Time for your LC/MS or GC/MS data set
  • Set any selected tR as the reference and provide a resolution parameter
  • Relative retention time column information now added to the Table of Peaks, Table of Structures, and Table of Mass Chromatograms
• Set the Retention Time Offset in order to align traces multiple detectors
  • The offset is automatically added to the spectrum parameters
  • The current offset settings can be automatically applied to newly opened data files
• Annotate automatically chromatogram peaks with their Base Peak Mass value
• Updated exact mass values for all radioactive isotopes
• View the peak integration areas in the Table of Peaks, which can be exported or copied through the Clipboard

VI) Data display and interface navigation were improved to better fit your work habits

• Switch between as many as fifty windows, with the assurance that the program remembers the processing position and state in each case when you switch back
• Improved Synchronization mode across different module windowpanes
• Synchronize according the Retention Time scale
  • Entering COMPARELCMS mode automatically synchronizes the data sets by retention time for improved confidence of data extraction
• Focus on the region of interest by predefining the display ranges for the mass spectra and chromatogram windowpanes. This range is automatically mirrored in the corresponding reports
• Chromatogram and spectral display has been enhanced for situations where there is low spectral noise

VII) Compare mass spectrometry spectra through a correlation analysis algorithm for finding similarity and dissimilarity between spectra (more details):

• Extract information and correctly identify homologous series even from low concentrations that generate a weak signal
• Perform Auto-correlation, Cross-correlation, and Component Detection on a single spectrum, or partial or whole LC/MS data sets
  • Detect even low intensity fragments' isotope cluster patterns* (^35/37Cl, ^79/81Br, etc.) and homologous compounds
  • Identify similar mass spectra from similar compounds

VIII) Data processing was improved and optimized

• Entering CODA and COMPARELCMS remembers previous mass chromatograms calculations and does not clear these values unless the algorithm is run again
• Restrict processing to only the zoomed region. For example, CODA, COMPARELCMS, and Correlation Analysis can be selectively applied to only those regions of interest
• Create an averaged data set from multiple LC(GC)/MS data sets
• Sum extracted mass chromatograms
  • Select several mass chromatograms interactively from the spectra or pick entire regions
• Perform the combine operation with a minimum of one scan for peak average and background subtraction
• The COMPARELCMS Option dialog box was augmented with CODA Baseline Correction and Peak Picking set options (more details)
• Enter fractional values for the Ratio Level parameter in the COMPARELCMS options. For example, components that change by more than 25% would be found if we entered 0.25 as the ratio level (more details)

IX) Automate repetitious processing tasks through an expanded series of Macro Commands:

• Calculate mass chromatograms through macro commands
• Pass a spectrum parameter or user data to a macro
• Export the TIC or specific mass chromatograms to ACD/ChromManager with a macro command
• Perform different Correlation Analyses through macro commands (more details)