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.

In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push towards technologies capable of resolving such biological complexity at the molecular level. While RNA-based approaches have long been the method of choice, advances in mass spectrometry (MS)-based technologies have led to the ability to resolve cellular proteomes within minute sample quantities and, very recently, even down to a single cell. Current limitations are the incomplete proteome depth achieved and low sample throughput, and continued efforts are needed to push the envelope on instrument sensitivity, improved data acquisition methods, and chromatography. 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 and improved 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 (DIA) on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and WhisperTM flow chromatography are well-tailored for low-input proteomics experiments. They can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples, cellular sub-populations, and eventually, scMS.