From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal peptide or vice versa?
Signal peptides are typically at the N terminus of a protein and are processed by the translocon machinery and are cleaved off after sorting through the membranes of organelles in the secretory system:
- endoplasmic reticulum
- Golgi apparatus
- ER-Golgi transition vesicles
- plasma membrane
Transit peptides target the protein to other subcellular organelles such as (from UniProt):
N-terminal transit peptides are quite rare. C-terminal transit peptide motifs are much more common. UniProt holds transit peptides as a discrete controlled vocabulary, separate from signal peptides.