Before acquisition, chromatographers often separate complex samples by a physical property such as hydrophobicity at high pH, charge, or size into discrete fractions before running standard LC/MS/MS analysis (where peptides are separated by hydrophobicity at low pH). With this preparation, the LC/MS/MS run produces an individual raw file for each fractionated file of the sample.
NOTE
Label-free quantification users must order fractions when adding them to a study. The application only performs retention-time alignment and feature mapping between the corresponding fractions in a fractionated sample. For example, the application can align fraction 1 across all samples, where all fraction 1’s contain the same peptide. For information on ordering fractions, see Assign the order of fractions.