Table 1.
Timing and difficulty level of different sample preparation protocols for MS-based proteomics
| Procedurea | FASP | SDS-ISD | SDC-FASP | SDC-ISD | OP-ISD | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Timing (h) | Difficulty levelb | Timing (h) | Difficulty level | Timing (h) | Difficulty level | Timing (h) | Difficulty level | Timing (h) | Difficulty level | |
| Protein extraction | 1.5 | ★★★ | 1.5 | ★★★ | 1.5 | ★★★ | 1.5 | ★★★ | 1.5 | ★★★ |
| Protein quantification | 1 | ★ | 0.5 | ★ | 1 | ★ | 1 | ★ | 1 | ★ |
| Clean up at protein level | 1.5 | ★★ | 9 | ★★★★ | 1 | ★☆ | 0 | – | 0 | – |
| Reduction and alkylation | 0.5 | ☆ | 0.5 | ☆ | 0.5 | ☆ | 0.5 | ☆ | 0 | – |
| Clean up at peptide level | 0 | – | 0 | – | 0.5 | ★ | 0.5 | ★ | 0.5 | ★ |
| Digestion | 7 | ★☆ | 6 | ☆ | 7 | ★☆ | 6 | ☆ | 6 | ☆ |
| Total | 11.5 | ★★★★ ★★★ ☆☆ |
17.5 | ★★★★ ★★★★ ☆☆ |
11.5 | ★★★★ ★★★ ☆☆☆ |
9.5 | ★★★★ ★ ☆☆ |
9 | ★★★★ ★ ☆ |
aprotein quantification can be performed by several methods. The timing is calculated from the method that required least time to be done, i.e. BCA methods for FASP, SDC-FASP, SDC-ISD and OP-IS protocols and Qubit for SDS-ISD
bThe difficulty level reflects the time required, the number of steps to be performed and the complexity of the steps; an open star indicates the easiest step, while the number of filled stars shows the level of difficulty of each step