High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps
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High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps. / Phlairaharn, Teeradon; Grégoire, Samuel; Woltereck, Lukas R.; Petrosius, Valdemaras; Furtwängler, Benjamin; Searle, Brian C.; Schoof, Erwin M.
In: Journal of Proteome Research, Vol. 21, No. 11, 2022, p. 2815-2826.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps
AU - Phlairaharn, Teeradon
AU - Grégoire, Samuel
AU - Woltereck, Lukas R.
AU - Petrosius, Valdemaras
AU - Furtwängler, Benjamin
AU - Searle, Brian C.
AU - Schoof, Erwin M.
N1 - Publisher Copyright: ©
PY - 2022
Y1 - 2022
N2 - In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyzer can sometimes be limiting. Therefore, low-input proteomics and scMS could benefit from linear ion traps, which provide faster scanning speeds and higher sensitivity than an orbitrap mass analyzer, however at the cost of resolution. We optimized an acquisition method that combines the orbitrap and linear ion trap, as implemented on a tribrid instrument, while taking advantage of the high-field asymmetric waveform ion mobility spectrometry (FAIMS) pro interface, with a prime focus on low-input applications. First, we compared the performance of orbitrap- versus linear ion trap mass analyzers. Subsequently, we optimized critical method parameters for low-input measurement by data-independent acquisition on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and Whisper flow chromatography are well-tailored for low-input proteomics experiments, and can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples and cellular subpopulations.
AB - In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyzer can sometimes be limiting. Therefore, low-input proteomics and scMS could benefit from linear ion traps, which provide faster scanning speeds and higher sensitivity than an orbitrap mass analyzer, however at the cost of resolution. We optimized an acquisition method that combines the orbitrap and linear ion trap, as implemented on a tribrid instrument, while taking advantage of the high-field asymmetric waveform ion mobility spectrometry (FAIMS) pro interface, with a prime focus on low-input applications. First, we compared the performance of orbitrap- versus linear ion trap mass analyzers. Subsequently, we optimized critical method parameters for low-input measurement by data-independent acquisition on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and Whisper flow chromatography are well-tailored for low-input proteomics experiments, and can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples and cellular subpopulations.
KW - data acquisition
KW - FAIMS-MS
KW - low-input applications
KW - mass spectrometry
KW - peptide identification optimization
KW - ultrasensitive proteomics
U2 - 10.1021/acs.jproteome.2c00376
DO - 10.1021/acs.jproteome.2c00376
M3 - Journal article
C2 - 36287219
AN - SCOPUS:85140958802
VL - 21
SP - 2815
EP - 2826
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
IS - 11
ER -
ID: 325637033