Protein quantification is a crucial data processing step that combines quantitative values at the peptide or fragment level into protein levels in mass spectrometry-based proteomics. However, many of ...

Mass spectrometry (MS) has emerged as an imperative technology in protein and peptide bioanalysis, offering unparalleled sensitivity, specificity, and dynamic range. However, the complexity of MS dat...

Charge detection mass spectrometry (CDMS) enables direct measurement of mass and charge for individual ions and overcomes fundamental limitations of conventional electrospray mass spectrometry for lar...

Electrospray ionization (ESI)-based native mass spectrometry (MS) has been extensively used to study non-covalent protein complexes and their structural aspects in the gas phase. As such it has a stab...

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...

ALT: a close up of a man in a suit and tie with a question mark on his neck .

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.....