Table 5.
Performance comparison among various 1D, 2D, and 3D-LC systems.
| Sample | MS | Paramater | 1D | 2D | 3D | Reference |
|---|---|---|---|---|---|---|
| HEK 293T cells | Orbitrap Fusion | Sample amount (µg) | 6 | 30 | 30 | [69] |
| Setup | RP | SAX-RP | SAX-RP-RP | |||
| Id. proteins | 4275 ± 26 | 5380 ± 88 | 8222 ± 109 | |||
| Id. unique peptides | 19,768 ± 333 | 34,912 ± 925 | 74,432 ± 996 | |||
| Fraction number | 1 | 3 | 11 | |||
| MS time (h) | 1.4 | 4.2 | 20.4 | |||
| Jurkat cells | TripleTOF 5600 | Sample amount (µg) | 1 | 200 | 720 | [61] |
| Setup | RP | RP-RP | RP-RP-RP | |||
| Id. proteins | 2568 | 8757 | 14,230 | |||
| Id. unique peptides | 11,878 | 109,461 | 251,166 | |||
| Fraction number | 1 | 21 | 126 | |||
| MS time (h) | 1.5 | 31.5 | 189 | |||
| HeLa cells & K562 cells | LTQ-Orbitrap Velos | Sample amount (µg) * | 125 and 750 | 500 and 3000 | 500 | [67] |
| Setup | RP | HILIC-RP | SCX-HILIC-RP | |||
| Unique phos.pro. * | 1570 and 1763 | 3891 and 4132 | 3424 and 4708 | |||
| Unique phos.pep. * | 3726 and 4104 | 16,637 and 16,722 | 11,980 and 22,148 | |||
| Fraction number | 1 | 20 | 63 | |||
| MS time (h) | 2 | 40 | 126 | |||
| Mouse embryonic fibroblast | AB Sciex QSTAR XL QTOF | Sample amount (µg) | 15 | 15 | [83] | |
| Setup | RP-RP | RP-SCX-RP | ||||
| Id. proteins | 2358 | 3114 | ||||
| Id. unique peptides | 13,573 | 25,792 | ||||
| Human urine | TripleTOF 5600 | Sample amount (µg) | 20 | 200 | 5000 | [60] |
| Setup | RP | RP-RP | GELFrEE-RP-RP and LPIEF-RP-RP | |||
| Id. proteins | 808 | 3162 | 6085 | |||
| Id. unique peptides | 13,895 | 25,940 | 68,151 | |||
| Fraction number | 1 | 20 | 360 | |||
| MS time (h) | 2 × 3 | 40 | 720 | |||
| Mouse brain | Q-Exactive HF | Sample amount (µg) | 500 | 500 | [51] | |
| Setup | RP-RP | SCX-RP-CZE | ||||
| Id. proteins | 8900 | 8200 | ||||
| Id. unique peptides | 70,000 | 65,000 | ||||
| Fraction number | 30 | 60 | ||||
| MS time (h) | 60 | 70 | ||||
| E. coli | LCQ Deca XP ion trap | Sample amount (µg) | 20 | 20 | [80] | |
| Setup | RP-RP | RP-SAX-RP | ||||
| Id. proteins | 702 | 923 | ||||
| Id. unique peptides | 2923 | 4254 | ||||
| Fraction number | 40 | 37 | ||||
| MS time (h) | 80 | 74 |
Identified proteins are those with at least two peptides. * Two numbers in each position are for HeLa cells and K562 cells, respectively. Id.: Identified; phos.pro.: phosphoproteins; phos.pep.: phosphopeptides.