Table 1.
Experimental overview to assess the advanced platform performance in part and overall
| Platform Constituent Assessed | Question | Display item |
|---|---|---|
| LC setup | Packed columns vs μPAC | Fig. 2 |
| Comparison of different μPACs | Fig. 3 | |
| Protein IDs/min and throughput | Fig. 4 and Table 2 | |
| MS acquisition | WWA vs DDA | Fig. 5A, B |
| Isolation width evaluation for WWA | Fig. 5D, E | |
| Search engine | CHIMERYS vs classical search engine | Fig. 5A–C |
| Entrapment experiment for FDR estimation | Fig. 5C | |
| Application – low input & single cells | Influence of WWA + /− MBR on protein IDs and quantification for (very) low inputs | Fig. 6A–D |
| Application - two-species proteome mix | Evaluation of quantitative accuracy for DDA and WWA using CHIMERYS | Supplementary Fig. 6 |
| Application – AP-MS – entire workflow | Impact of entire workflow (μPAC, WWA, CHIMERYS) on identification of additional interaction partners in AP-MS | Fig. 7 and Table 3 |