Table. 1 TOFIMS method optimized for immunopeptidomics
From: TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification
MS parameter | Setting | |
|---|---|---|
source | Source | captive spray |
Capillary | 1500 V | |
TIMS settings | 1/k0 start to end (locked) | 0.6–1.6 Vs/cm2 |
Ramp time | 200 ms | |
Accumulation time | 200 ms | |
Duty cycle (locked) | 100% | |
Ramp rate | 4.85 Hz | |
tune | Collision energy | 10 eV |
Collision RF | 1500 Vpp | |
Transfer time | 60 µs | |
Pre pulse storage | 6 µs | |
Mass spectra peak detection | ||
Absolute threshold | 10 | |
Absolute threshold (per 100 ms accu time) | 5 | |
PASEF data | ||
Denoising mode | No reduction | |
Mobility peak detection | ||
Absolute threshold | 5000 | |
MS/MS | Number of PASEF ramps | 6 |
Total cycle time | 1.44 s | |
Charge | 0–5 | |
Scheduling | Linear | |
Precursor repetition | ||
Target intensity | 20,000 | |
Intensity threshold | 1000 | |
Active exclusion | Activated | |
Release after | 0.4 min | |
Collision energy settings | ||
1/k0 | 0.6–1.6 Vs/cm2 | |
20–59 eV | ||
MS | m/z | 100–2000 |
Polarity | Positive | |
Scan mode | PASEF |
