Digital quadrupoles are driven with rectangular RF waveforms and, through duty cycle control, can access higher-order Mathieu space stability zones (HZs) using comparatively low voltages. Analytically...

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Stable electrospray ionization is crucial for ensuring consistent ion generation in mass spectrometry. Previously, a feedback control system based on …

Stable electrospray ionization is crucial for ensuring consistent ion generation in mass spectrometry. Previously, a feedback control system based on …

High-resolution mobility-based ion separations in Structures for Lossless Ion Manipulations (SLIM) have been useful for ion mobility separations for a variety of molecular classes in the gas phase. He...

Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for data-independent acquisition (DIA), we developed a second version of our framework for data-driven optimization of MS methods (DO-MS). The DO-MS app v2.0 (do-ms.slavovlab.net) allows one to optimize and evaluate results from both label-free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant to single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication of quality figures that can be easily shared. The source code is available at github.com/SlavovLab/DO-MS.

In mass spectrometry (MS), the radio frequency (RF)-only multipole ion guide commonly used in a medium pressure range (0.1–10 Pa) is susceptible to a collision-damping-induced loss of instrumentation ...

The effectiveness of collision-induced dissociation (CID) in ion trap mass spectrometry (ITMS) is limited by a low-mass cutoff and weak fragmentation yields. Theoretically, the q value is optimized to...

In the last few years, high-resolution time-of-flight mass analyzers (TOF-MA) have been intensively developed. Their development requires tools that p…

In order to transport ions from an intermediate-pressure collisional cooling device to a planar electrostatic ion trap (PEIT) mass analyzer in an ultrahigh-vacuum chamber, a segmented radio frequency ...

A rather interesting post on AI's ability to actually do real physics research that beginning graduate students are expected to do. More th...

We have developed an electron-activated dissociation (EAD) device with product isolation functionality for multistage tandem mass spectrometry (MSn). The EAD portion is a branched magneto-radio freque...

Here, we describe ion confinement based on mobility in rotating electric fields under low E/N conditions. To do this, we constructed a device with a stack of eight segmented ring electrodes to which s...

The first results of using a new type of ultrahigh-resolution mass analyzer based on a planar multipass time-of-flight mass spectrometer with periodic reflecting lenses (Y-MRT MS) for bottom-up whole-...

Glycosylation, the enzymatic addition of carbohydrate moieties to proteins, is essential for immune recognition, protein folding, and disease progression. The structural complexity of glycans and the...

Rationale Proton transfer reaction mass spectrometry (PTR-MS) is a widely used technique for on-line detection of volatile organic compounds (VOCs). Sensitivity enhancement is an important developme.....

Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

Cyclic ion mobility spectrometry (cIMS) provides the potential for high resolution separations of small molecule isomers using multiple passes in a closed-loop geometry. Achieving this potential, howe...

An open-source platform for data-independent acquisition proteomics adapts predicted libraries to experimental settings.

Limited sensitivity and depth of proteome sampling in experiments using data-dependent acquisition (DDA) mass spectrometry are usually attributed to an insufficient rate of fragmentation spectra acquisition relative to the number of coeluting potential targets. Here, we demonstrated that limited sensitivity and dynamic range of MS1 scans reduce detection of low-intensity ions and thus their selection for fragmentation. As abundant ions occupy a large fraction of the ion accumulation capacity, we sought to improve MS1 detection of rare analytes by an easily implementable strategy based on gas-phase segmentation of the MS1 scan range, followed by coaccumulation and detection of all ions. The quadrupolar isolation windows used to segment the MS1 scan range are designed to transmit, on average, an equal number of charges, consistent with the parameter used by many recent mass spectrometers to regulate ion trap filling. This strategy, which we named high dynamic range MS1 (HDR-MS1), reduces the contribution of abundant ions to reaching the maximum ion capacity. As a result, HDR MS1 showed improved dynamic range and sensitivity compared to conventional full-range scans, resulting in a higher number of peptides and protein identifications under identical MS2 parameters, less redundant precursor ion sampling, and a higher rate of quantified precursor ions. HDR MS1 scans are compatible with any DDA precursor selection filter and MS2 parameter, and the generated files can be analyzed using any software for peptide-spectral matching and quantification.

There are many potential advantages to performing ion manipulations at atmospheric pressure (AP) compared to in vacuum. However, the RF electric fields commonly employed in vacuum-based systems are mo...