Table 2. Identification of endogenous peptides in the conditioned media by LC-MS/MS according to the total number of unique peptides and spectral counts.
| Accession number | Protein Identification | Experiment 1 | Experiment 2 | ||||||||||||||
| HaCaT | HaCaT+ PMA | SCC-9 | SCC- 9+PMA | HaCaT | HaCaT+ PMA | SCC-9 | SCC-9+ PMA | ||||||||||
| Run 1 | Run 2 | Run 1 | Run 2 | Run 1 | Run 2 | Run 1 | Run 2 | Run 1 | Run 2 | Run 1 | Run 2 | Run 1 | Run 2 | Run 1 | Run 2 | ||
| IPI00002441 | Syndecan-1 | 2/5 | 2/6 | 2/9 | 2/9 | 3/8 | 4/12 | 6/23 | 4/20 | 1/3 | 1/2 | 2/8 | 3/8 | 3/13 | 2/10 | ||
| SQGLLDRKEVLGGVIAGGLVG | 3 | 4 | 6 | 6 | 4 | 5 | 8 | 9 | 3 | 2 | 3 | 6 | 8 | 7 | |||
| SQGLLDRKEVLGGVIAGGLVGLI | 2 | 2 | 3 | 3 | 3 | 4 | 5 | 4 | 5 | 1 | 3 | 3 | |||||
| SQGLLDRKEVLGGVIA | 1 | 2 | 5 | 5 | |||||||||||||
| LDRKEVLGGVIAGG | 2 | 1 | |||||||||||||||
| SQGLLDRKEVLGGVIAGG | 1 | ||||||||||||||||
| RNQSPVDQGATGASQGLLDRKE | 2 | 2 | 2 | ||||||||||||||
| VLGGVIAGGLVG | |||||||||||||||||
| DLHTPHTED | 1 | ||||||||||||||||
The HaCaT and SCC-9 cells were treated with PMA for 24 h, the media were collected and the endogenous peptides were analyzed by LC-MS/MS. The total numbers of the unique peptides and the number of spectral counts are shown in bold and the number of spectral counts is shown for each sequence. There is a statistically significant difference in the number of spectral counts of syndecan-1 fragments between SCC-9 cells and SCC-9 cells treated with PMA (Mann-Whitney test, p = 0.0273).