Frequently Asked Questions

MS Manager

Q: What file formats can ACD/MS Manager import?

A: A complete list of supported file formats is available here.

Q: Is there is a change of mass accuracy when data is imported to MS Manager?

A: There is no loss of mass accuracy when data is imported to MS Manager. You can change the displayed number of decimal places for fractional masses of m/z values on mass spectra in the following manner: from the Options menu, choose Preferences, click the Peaks tab, and, from the Decimal Places list, select the correct number of Decimal Places.

Occasionally Thermo Xcalibur data, usually high resolution accurate mass data acquired in profile mode, will show mass spectra in Xcalibur where m/z values for peaks have fractional masses that are different from the ones displayed in MS Manager. MS Manager typically displays the m/z value of the data point corresponding to the peak maximum whereas Xcalibur will display a value that is calculated as the centroid of the profile peak, which may be different from the peak top. The Xcalibur centroid value is not available in the MS Manager software but an entire centroid spectrum can be easily created instead through the Process menu, choosing Create Centered Spectrum, and setting the desired conversion settings, e.g., Minimum FWHM 2 points, Abundance Threshold 0.0%, Center Method Mass Values using Top of peak, Abundance by Height, then click OK. The m/z values in the centroid spectrum of MS Manager should then be very close to, or the same as, those shown on the peaks in Xcalibur.

Q: Where can I find additional information about my experiment?

A: To find information about Instrument parameters, such as acquisition date, ionization mode, and sample information, from the View menu, choose Parameters. Additional information from Waters MassLynx files may also be available, from the View menu, choose User Notes.

Q: I canít import Applied Biosystems/Sciex data


  1. Check the version of Analyst. Currently, Analyst 1.4.x is supported, but Analyst 1.5 is not (May 20, 2009). A list of up-to-date formats is available here.
  2. Some MS/MS data from Analyst 1.4.x is not imported correctly. We are working on it with Sciex (May 20, 2009)
  3. If you are working with MS/MS data away from the instrument computer, you need both *.wiff and *.wiff.scan files present in the same folder to open the data. (Not all *.wiff files have an associated *.wiff.scan file)
  4. You may need to reregister the Wiff file format by uninstalling and reinstalling ACDWIFF.exe
    1. From the Windows Start menu, choose Run.
    2. Browse to the location of your ACD/Labs software installation, and choose ACDWIFF.EXE. In the Open line, type Ď /uninstallí.
    3. Click OK.
    4. From the Windows Start menu, choose Run.
    5. Browse to the location of your ACD/Labs software installation, and choose ACDWIFF.EXE. In the Open line, type Ď /installí.
    6. Click OK.

Q: I canít import my Agilent data files.


  1. If the files are Agilent *.wiff files, see the instructions on how to register the wiff filter described in section 2.d
  2. You may need to reregister the Agilent data format.
    1. From the Windows Start menu, choose Run.
    2. Browse to the location of your ACD/Labs software installation, and choose ACDAGILENTREG.EXE. In the Open line, type Ď /uninstallí.
    3. Click OK.
    4. From the Windows Start menu, choose Run.
    5. Browse to the location of your ACD/Labs software installation, and choose ACDAGILENTREG.EXE. In the Open line, type Ď /installí.
    6. Click OK.
  3. Make sure you have Microsoft .NET Framework version 2.0 or higher on your computer.
  4. If you want to send data to ACD/Labs, note that we need the full *.D folder to import the Agilent files.
  5. If Agilent MassHunter software was used, we can only import the raw data files. We cannot import data that has been previously processed by MassHunter.

Q: Can I apply a Waters MassLynx LockMass correction?

A: No, LockMass correction cannot be automatically applied upon import into ACD/MS Manager. The LockMass data is split into a different *.esp files, and there is currently no way to automatically make the correction.

Q: Thermo Xcalibur Data: How do I select the correct options for the Xcalibur splitter?

A: This will depend on your experiment, and how you want to open the data. The checkboxes on the left show the experiment parameters you can choose. On the right, each Data Set check box indicates a separate ACD/Labs *.esp file. You can expand the list to see which experiments will be included in the file.
For example, for a data-dependent experiment, we can split the file into the full-scan LC/MS1 data, and a second MS2 file.

Selecting the All Features check box on the left will create a *.esp file for each MS2 precursor ion.

Q: I want to display information about my file or data on top of the spectrum the way I do with my vendor software.


  1. To see file information in a table, from the View menu, choose Parameters
  2. From the Options menu, choose Header Information. Click Add. In the Category column, click on a cell twice. A drop-down menu appears. Choose Parameters. In the Data Names column, click on the cell twice. From the drop-down menu, choose the name of the data field you want to display. Click Apply or OK.

Q: How can I synchronize two spectra or chromatograms?

A: If you are in tab mode, double-click on the tab to switch to tile mode. Click to select the first file. Next, hold down SHIFT, and click the second file. In the upper right corner of the screen, click Synchronize. Use the zoom functions as normal.

Q: There are too many peak labels on my chromatogram


  1. From the Options menu, choose Preferences. In the Preferences dialog box that appears, click the Labels tab. From the drop-down menu, choose Chromatogram. Unselect the check boxes for the labels you wish to remove (e.g., BPM is base peak mass)
  2. You may need to adjust your peak picking options (see data processing section)

Q: My tables are in the way, and I canít see the spectrum.

A: Many, but not all of the tables can be docked. To dock a table, mouse over the blue title bar. Click and drag the table to the upper (or lower) left corner of the screen. Aim for the corner between the macro Organizer toolbar, and the file. When you see the window dock, release the mouse button.

Q: I want to perform a function, but I canít find the button. Where did it go?

A: Make sure the appropriate window is active, e.g., the chromatogram window must be active to select chromatogram processing functions like IntelliXtract, CODA, etc. The mass spectrum window must be active for mass spectrum functions like AutoAssignment, Formulae Generator, etc. Simply click the appropriate window to make it active.

Q: There are too many/not enough peaks picked during Peak Picking, CODA, or IntelliXtract.

A: Click the Options button, and in the Peak Picking options, increase/decrease the Minimum FWHM value

Q: How do I add a peak label on the shoulder of a peak on the TIC?

A: Enter Peak Picking mode, and select Peak by Peak. Hold down SHIFT, mouse over the chromatogram, and click to mark the peak.

Q: Does AutoAssignment work with high-resolution data?

A: Yes. You can adjust the mass accuracy for assignment according to your data. From the Options menu, choose Mass Accuracy, and modify the Assignment value. For ion trap or quadrupole data, we recommend an assignment accuracy of 0.2-0.5 Da. For TOF data, we recommend 0.02-0.05 Da. For Orbitrap or FTMS data, we recommend 0.002-0.005 Da.

Q: The fragment of interest was not predicted by AutoAssignment.

A: In Assignment mode, click Options, and select the Reactions tab. You can try to increase the Maximum number of Fragments Generated on Each Step (10-30 000), or increase the Number of Fragmentation Steps (4-5). You might also consider switching on some of the Specific Fragmentation rules that are off by default. If you increase the number of selected rules, you should also consider increasing the Maximum Number of Fragments Generated on Each Step as well.

AutoAssignment is a rules-based predictor, and is based on well-documented fragmentation rules reported in the literature. It is possible that the fragment isn't predicted by the fragmentation rule set.

Q: How can I extract an ion chromatogram?

A: Click the chromatogram window to make it active. Next, click Mass Chrom. Click Run, and type the m/z value of interest.

Q: I cannot add my mass spectrum to the database.

A: A database must be open, and in Update mode. Click Database to switch to the database window. From the File menu, choose Open or New. Click Switch User Database to Update Mode. Return to the Processor window, and update the spectrum.

Q: I cannot add my chromatogram to the database.

A: Chromatograms cannot be added to MS Manager databases. To add chromatograms, you will need to install ACD/ChromManager, the chromatography module, or ACD/MS Manager Suite, which includes ChromManager.