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?
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Signal peptides are typically located at the N terminus of a protein. The signal peptides 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
- lysosomes
Transit peptides target the protein to other subcellular organelles such as (from UniProt):
- Mitochondrion
- Apicoplast
- Chromoplast
- Chloroplast
- Cyanelle
- Thylakoid
- Amyloplast
- Peroxisome
- Glyoxysome
- Hydrogenosome
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.