For precursor ion quantification and label free quantification, you must specify the order of the fraction numbers for the files in an input file set. In addition, you must perform retention-time alignment and feature mapping only between files that have the same fraction number.

Reporter ion quantification handles fraction order automatically.

The Input Files page of a study displays the fraction numbers. It consists of a table that lists the identification number (ID) of a file, the path and name of the file, the modification date, and the size of each file in the file set. The IDs include the file number followed by a period and then the fraction number. For example, the ID F21.3 represents file 21 and fraction 3.

Procedure

  1. Add the file set to the study. See Add fractions.
  2. Select the Input Files tab.
  3. Select Show Details at the bottom left corner.
  4. Select Define Fraction Numbers on the Input Files page.
  5. This button is available when the input file set contains multiple files and is not a subset of another file set.
  7. The Specify File Fractions dialog box opens, which lists all the files in a file set. The following image shows the files not in numerical order.
  9. Sort the files by doing one of the following:
  10. Select Sort to sort the fractions automatically by the selected file part.
  11. The application sorts file names numerically when all the selected file parts start with a numeric value; otherwise, it sorts them alphabetically.
  12. Use the arrow keys to the right of Select Difference to Sort By:, , to highlight the part of the file name to sort by.
  13. When there are multiple different file parts, you can select a file part by clicking the arrows; the selected file part is highlighted in blue, while other parts are highlighted in gray.
  14. –or–
  15. Manually change the fraction numbers by dragging the file names. Use the variable placement handle, , to drag each file.
  16. The files are now in numeric order.
  18. Select Ok to close the dialog box and store the new fraction numbers, or select Cancel to restore the previous fraction numbers.