Table I. Comparison of instruments. The table presents the number of PSMs, unique peptide readings, and number of proteins identified with the different instruments using Mascot search engine at 1% protein FDR. IPG-IEF, immobilized pH gradient isoelectric focusing; PSM, peptide spectrum match; The table is based on IPG-IEF using 400 μg loaded peptide amount, analyzing fractions 32–36 with a 45 min LC gradient.
| Instr. | Identification |
Quantification |
||
|---|---|---|---|---|
| PSM | PSM | Peptides | Proteins | |
| Orbitrap | 19512 | 11022 | 4153 | 2453 |
| MALDI | 1074 | 1039 | 816 | 620 |
| QTOF | 1818 | 1765 | 290 | 238 |