Table 1.
LC-MS/MS analysis results of the tryptic digests prepared by different sample preparation workflows for MDDC Triton X-100 cell lysate and RIPA cell lysate. Data reported here are the average results over four experimental replicates for each workflow (two technical replicates of each experimental replicate were merged). Identification FDR threshold for MS/MS spectra is 5% (local FDR), for distinct peptides is 5% (local FDR) and for proteins is 1% (global FDR). Only the distinct peptides that are associated with the confidently identified proteins are included in the results.
|
Cell
lysate |
Sample preparation workflow (n=4) |
MS/MS spectra | Distinct peptides |
Protein (CV%) |
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Total (CV%) |
Identified (CV%) |
% of identified |
Total (CV%) |
Fully cleaved (CV%) |
% of fully cleaved |
Missed cleavage |
||||
| 1 | ≥2 | |||||||||
| Triton X-100 (TCL) |
pA-sT | 52748 (3.4) |
26227 (4.1) |
49.7 | 5563 (5.4) |
5332 (5.7) | 95.8 | 222 | 9 | 880 (4.0) |
| pAwA-sT | 42864 (5.4) |
21791 (8.1) |
50.8 | 5045 (4.0) |
4898 (3.9) | 97.1 | 144 | 4 | 791 (6.2) |
|
| pAwA-sTS | 52485 (7.1) |
19948 (14.9) |
38.0 | 3770 (6.7) |
3658 (6.4) | 97.0 | 110 | 1 | 687 (6.9) |
|
| pAwA-sTD | 42880 (4.1) |
23969 (6.0) |
55.9 | 5612 (3.0) |
5378 (3.1) | 95.8 | 228 | 7 | 941 (2.0) |
|
| RIPA (RCL) |
pA-sT | 49978 (6.0) |
27125 (4.8) |
54.3 | 5675 (4.3) |
5449 (4.7) | 96.0 | 220 | 7 | 908 (1.8) |
| pAwA-sT | 43297 (1.9) |
23354 (3.9) |
53.9 | 5372 (4.8) |
5196 (5.6) | 96.7 | 172 | 4 | 838 (5.4) |
|
| pAwA-sTS | 47590 (7.6) |
21734 (10.7) |
45.7 | 4117 (5.3) |
3985 (5.2) | 96.8 | 130 | 2 | 771 (4.9) |
|
| pAwA-sTD | 43274 (1.6) |
25908 (2.0) |
59.9 | 5676 (2.9) |
5442 (3.0) | 95.9 | 227 | 7 | 959 (4.7) |
|