Strengths and weaknesses of different AP-MS approaches
| Strength/weakness | Tagged cDNA | Specific antibodiesc | QUBIC | |
| Single-step purificationa | TAP purificationb | |||
| Endogenous gene expression level | − | − | + | + |
| Endogenous gene processing | − | − | + | + |
| Material required | + | − | + | + |
| Transient interactors | + | − | +/− | + |
| True quantification for background discrimination | +/− | + | +/− | + |
| Objective statistical evaluation | +/− | +/− | +/− | + |
| Sensitivity | + | +/− | − | + |
| Measurement time | +/− | + | − | + |
| Standard protocol for all baits | +/− | +/− | − | + |
| Compatible with imaging methods | +/− | +/− | − | + |
| Strength/weakness | Tagged cDNA | Specific antibodiesc | QUBIC | |
| Single-step purificationa | TAP purificationb | |||
| Endogenous gene expression level | − | − | + | + |
| Endogenous gene processing | − | − | + | + |
| Material required | + | − | + | + |
| Transient interactors | + | − | +/− | + |
| True quantification for background discrimination | +/− | + | +/− | + |
| Objective statistical evaluation | +/− | +/− | +/− | + |
| Sensitivity | + | +/− | − | + |
| Measurement time | +/− | + | − | + |
| Standard protocol for all baits | +/− | +/− | − | + |
| Compatible with imaging methods | +/− | +/− | − | + |
+, fulfilled; +/−, partially fulfilled; −, not fulfilled. Three common AP-MS strategies are summarized and compared with QUBIC. There are different aspects that facilitate reliable and scalable results in MS-based interaction mapping. Before QUBIC, it is possible to meet some but not all of these requirements at the same time.
Sowa et al., 2009.
Glatter et al., 2009.
Trinkle-Mulcahy and Lamond, 2007.