Table 2. Proteins and Unique Peptides Identified by X!Tandem and Andromeda in the hSAX and High pH RP LC–MS Experiments from RAW264.7 Cell Lysate.
| separation | search engine | unique proteinsa | unique peptidesb |
|---|---|---|---|
| 1D-SAX | X!Tandem | 9469 | 126318 |
| 1D high pH RP | X!Tandem | 8627 | 99110 |
| combined | X!Tandem | 9871 | 159847c |
| 1D-SAX | Andromeda | 8830 | 116093 |
| 1D high pH RP | Andromeda | 8131 | 95721 |
| combined | Andromeda | 9613 | 154553 |
a
Unique proteins (FDR ≤ 1%) according to ProteinProphet (X!Tandem) and MaxQuant (Andromeda).
b
Unique nonstripped peptides (FDR ≤ 1%) according to PeptideProphet (X!Tandem) and MaxQuant (Andromeda).
c
Number differing from Figure 4A due to FDR recalculation on combined pep.xml (PeptideProphet).