Table I. Endogenous peptide targets, corresponding internal standards, and selected transitions for monitoring NFκB subunits, Bcl-2 family members, and Fanconi Anemia DNA damage repair proteins. Residues underlined in bold font indicate the sites of incorporation of stable isotope labels or single conservative amino acid replacements. Stable isotope labeled amino acids include proline (13C5, 15N), valine (13C5, 15N), leucine (13C6, 15N), and tyrosine (13C9, 15N). Limits of quantification (LOQ) are estimated using the lower end of the linear range of the calibration curve for each peptide standard. Additional data are available online at http://proteome.moffitt.org/QUAD/66.
| Protein | Peptide (Label) | Transitions | LOQ (fmol) | Additional Peptides |
|---|---|---|---|---|
| NFκB-1, p105 | AGADLSLLDR (A → G) | y5–y8 | 0.1 | 3 |
| NIHLHAHSLVGK | y6–y10 | 5 | ||
| NFκB-1, p50 | NIHLHAHSLVGK | y6–y10 | 5 | |
| NFκB-2, p100 | AGAGAPELLR | y5–y9 | 0.1 | 5 |
| VGADPALLDR | y5–y9 | 0.1 | ||
| DSGEEAAEPSAPSR | b8, y8–y10 | 0.5 | ||
| NFκB-2, p52 | QYAIVFR (Q → N) | y3–y5 | 0.1 | |
| RelA, p65 | GSFSQADVHR | y4–y8 | 0.5 | 6 |
| DLEQAISQR (E → D) | y4–y7 | 0.1 | ||
| RelB | ADFSQADVHR | y3–y7 | 1 | 3 |
| Bcl-2 | FATVVEELFR | y5–y8 | 10 | |
| Bcl-xL | EAGDEFELR | y4–y7 | 0.5 | |
| Mcl-1 | QSLEIISR (E → D) | y3–y7 | 0.1 | 1 |
| Bfl-1 | VLQNVAFSVQK (A → G) | y4–y6, y9 | 5 | |
| Bad | GLGPSPAGDGPSGSGK | y10, y11, y13, y14 | 1 | |
| Bid | IEADSESQEDIIR (D → E) | y5–y11 | 0.1 | 1 |
| Bim | IGDEFNAYYAR | y4, y6, y7, y10 | 0.5 | |
| Bak | QLAIIGDDINR (A → G) | y6–y9 | 1 | |
| Bax | TGALLLQGFIQDR (A → G) | y6–y9 | 2 | |
| Fanc D2 | NSDEINIPR | y3–y7 | 0.1 | 6 |
| Fanc I | TIETSPSLSR | y5–y8 | 0.1 | 7 |