TABLE 1.
Phosphopeptides Identified by Targeted MRM-IDA
| α-Casein | |||
| Peptide | MH+ | Neg Prec 79 | Target MRM |
| DIGSESTEDQAMEDIK | 1846.71 | — | ✓ |
| DIGSESTEDQAMEDIK | 1926.00 | — | ✓ |
| YKVPQLEIVPNSAEER | 1950.95 | ✓ | ✓ |
| VPQLEIVPNSAEER | 1659.79 | ✓ | ✓ |
| TVDMESTEVFTK Oxidation (M) | 1481.60 | ✓ | ✓ |
| TVDMESTEVFTK | 1465.60 | ✓ | ✓ |
| KTVDMESTEVFTK | 1593.60 | ✓ | ✓ |
| KTVDMESTEVFTK Oxidation (M) | 1609.00 | ✓ | — |
| EQLSTSEENSK | 1330.50 | ✓ | ✓ |
| NMAINPSKENLCSTFCK Oxidation (M) | 2108.87 | — | ✓ |
| NMAINPSKENLCSTFCK | 2092.00 | ✓ | ✓ |
| 8 | 10 | ||
| MEF2A | |||
| Peptide | MH+ | Neutral Loss 49 | Target MRM |
| Nonphosphopeptides (false positives) | 16 | 3 | |
| SEPISPPR | 962.43 | — | ✓ |
| SEPSPPRDR | 1233.56 | ✓ | ✓ |
| VMPTKSPPPPGGGNLGMNSR | 2073.95 | ✓ | ✓ |
| GMMPPLSEEEELELNTQR | 2182.93 | ✓ | ✓ |
| GCDSPDPDTSYVLTPHTEEK | 2327.93 | ✓ | ✓ |
| QEMGRSPVDSLSSSSSSYDGSDR | 2514.00 | — | ✓ |
| Identified phosphopeptides | 4 | 6 | |
Targeted MRM-IDA method was able to identify more phosphopeptides than methods using neutral loss or precursor ion scans. This method was also more specific for phosphopeptide identification, in that it rarely triggered an MS/MS spectra for nonphosphorylated peptides. The phosphorylation site is indicated by an underscore.