Plasma membrane Intrinsic Proteins (PIPs), a subfamily of aquaporins, are ubiquitous membrane channel proteins that play a crucial role in water uptake in plants. The use of high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) analysis of peptides has previously shown to be a valuable tool to differentiate among PIP homologues sharing a high sequence homology and also to characterize their post-translational modifications (PTMs). The recent introduction of mass spectrometers able to measure peptide mass with high mass accuracy, together with new alternative ways of peptide fragmentation allows the identification and characterization of proteins from nonsequenced organisms, such as broccoli. In this study, we combined three endoproteases (trypsin, Glu-C and Lys-C) with HPLC-MS/MS analysis and two types of peptide fragmentations, CID (collision induced dissociation) and HCD (higher-energy C-trap dissociation), to identify PIP isoforms and PTMs from broccoli roots. After de novo sequencing analysis, eight peptides showing homology to Arabidopsis thaliana PIPs were identified. Although Arabidopsis nomenclature of PIP isoforms has not been defined for broccoli, our results agree with the occurrence of seven AtPIP isoforms (PIP 1;1, PIP 1;2, PIP 1;3 and PIP2;2, PIP 2;3, PIP2;1 and PIP2;7) in broccoli roots, as compared to the plant model A. thaliana. To our knowledge, these results represent the deepest characterization of the PIPs isolated from the roots of broccoli, a crop with increasing agronomical interest.