Exclusion and inclusion mass lists are lists of mass-to-charge ratios (m/z) that you want to exclude or include from tandem mass spectrometry (MS/MS).
You can export mass lists based on your current search results. You can export lists compatible with the LTQ Orbitrap, Q Exactive, or Orbitrap Fusion family of instruments. The mass lists from the three types of instruments differ in format.
Mass lists also differ in their usage. The Export Instrument_name Mass List dialog box contains two groups of parameters that you can use to customize the exported mass list. The parameters in the Items To Be Exported area specify which result items should be transferred to the mass list. The parameters in the Options area customize the format of the resulting mass list. Use these features to export to a format that you can use in the Xcalibur data system.
Procedure
- Open your search results in the result file. See Organizing results.
- From the main menu, select one of the following:
- To export mass lists compatible with the LTQ Orbitrap family of instruments, select File > Export > LTQ Orbitrap Mass List.
- The Export LTQ Orbitrap Mass List dialog box opens.
Export LTQ Orbitrap Mass List dialog box - –or–
- To export mass lists compatible with the Orbitrap Fusion family of instruments, select File > Export > Orbitrap Fusion Mass List.
- The following figure shows the Export Orbitrap Fusion Mass List dialog box for the Orbitrap Fusion Mass List.
Export Orbitrap Fusion Mass List dialog box - –or–
- To export mass lists compatible with the Q Exactive family of instruments, select File > Export > Q Exactive Mass List.
- The following figure shows the Export Q Exactive Mass List dialog box for the Q Exactive Mass List.
Export Q Exactive Mass List dialog box - In the Destination box, enter the path and name of the file where you want to save the exported mass list; or locate the file, select it, and select Save in the Save As dialog box.
- In the Items To Be Exported area, specify which result items are to be transferred to the mass list:
- From MS/MS Spectrum Info: Exports the precursor masses of all the spectra listed on the MS/MS Spectrum Info page of the result file.
- From PSMs: Exports the masses of all PSMs listed on the PSMs page of the result file.
- From Peptide Groups: Exports the masses of all PSMs of the peptide groups listed on the Peptide Groups page of the result file.
- From Proteins: Includes the Exports the masses of all PSMs of the proteins listed on the Proteins page of the result file.
- To export only certain data in the categories that you selected in the Items To Be Exported area, do the following:
- On the appropriate page of the result file, select the checkbox to the left of each item that you want to export. For information, see Check items on the pages of a result file.
- In the Export Instrument_name Mass List dialog box, select the Checked Items Only checkbox.
- If you do not select the Checked Items Only checkbox, the application exports all masses in the categories that you selected.
- In the Retention Time Window boxes in the Options area, specify the width of the retention time window, in minutes:
- In the To Left (min) box, specify the lower retention time limit, in minutes, that an item must have to be included in the mass list.
- In the To Right (min) box, specify the upper retention time limit, in minutes, that an item must have to be included in the mass list.
- You can have only n entries in the mass list per retention time window. Specify n with the Max Concurrent Entries parameter in the Export LTQ Orbitrap Mass List dialog box.
- (Export LTQ Orbitrap Mass List only) Select either the Export Uncharged Mass Values or the Export m/z Values option.
- Export Uncharged Mass Values: Determines whether the masses selected in the Items To Be Exported area are to be exported with their uncharged masses.
- Export m/z Values: Determines whether the masses selected in the Items To Be Exported area are to be exported with their detected m/z values.
- (Export LTQ Orbitrap Mass List only) In the Mass Precision (decimals) box, specify the number of decimals for each mass that appears in the mass list.
- (Export LTQ Orbitrap Mass List only) In the Max Concurrent Entries box, specify the maximum number of entries per given retention time window.
- (Optional) (Q Exactive Mass List or Orbitrap Fusion Mass List only) Select the Include A+1 and A+2 Masses checkbox.
- With this option, the application inserts mass entries for the A+1 and A+2 peak of the mass entry to prevent these ions from being detected by the device. This option ensures that not only the monoisotopic peak of an ion is excluded but also the first and second 13C peaks in the isotope pattern.
- The width of the window is specified by the Retention Time Window Width parameter.
- Select Export.
- Use a standard text editor to view the resulting mass list.
- The following figure shows an example of the mass list for LTQ Orbitrap instruments.
Exported mass list example for the LTQ Orbitrap - The following figure shows an example of the mass list for Q Exactive instruments. The Q Exactive format has column headers in the exported tab-separated text files and an additional column with the polarity information, which is always set to Positive.
Exported mass list example for the Q Exactive - The following figure shows an example of the mass list for Orbitrap Fusion instruments. The values in the Orbitrap Fusion format are separated by tabs. Values in the Start Time and End Time columns are in minutes, and values in the MassCharge column are in thomsons (Th).
NOTE
The thomson is defined as follows:
where:
u represents the unified atomic mass unit.
Da represents the dalton unit.
e represents the elementary charge that is the electric charge unit in the atomic unit system.
