Mike Goodwin

ASMS acceptances are coming out #TeamMassSpec

Spatial selection of ions separated in a multi-reflection time-of-flight mass analyzer Multi-reflection time-of-flight mass analyzers (MR TOF MAs) have become widely used in nuclear physics research due to their combination of high mass …

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Finally released the preprint covering TMT HR mode for the Orbitrap Astral Zoom mass spectrometer. Here, multi-pass MS/MS measurements grant us sufficient resolution to quantify TMT reporter ions even to 35-plex, greatly increasing analytical throughput.

www.biorxiv.org/content/10.6...

Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows Advances in mass spectrometry have enabled increasingly fast data-independent acquisition (DIA) experiments, producing datasets whose scale and complexity challenge existing analysis tools. Those same advances have also led to the use of narrow isolation windows, which alter MS2 spectra via fragment isotope effects and give rise to systematic deviations from spectral libraries. Here we introduce Pioneer and Altimeter, open-source tools for fast DIA analysis with explicit modeling of isolation-window effects. Altimeter predicts deisotoped fragment intensity as a continuous function of collision energy, allowing a single spectral library to be reused across datasets. Pioneer re-isotopes predicted spectra per scan and combines an intensity-aware fragment index, spectral deconvolution, and dual-window quantification for fast, spectrum-centric DIA analysis. Across instruments, experimental designs, and sample inputs, Pioneer enables high-confidence identification and precise quantification at scale, completing analyses 2-6x faster and maintaining conservative false-discovery rate control.

(BioRxiv All) Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows: Advances in mass spectrometry have enabled increasingly fast data-independent acquisition (DIA) experiments, producing datasets whose scale and complexity… #BioRxiv #MassSpecRSS

Regarding Emitter Positioning for Nanoflow Electrospray Ionization with a High-Capacity Inlet Capillary Nanoflow electrospray ionization is commonly used for proteomics due to its high sensitivity. Signal intensity, however, is dependent on optimal emitter positioning relative to the mass spectrometer i...

Regarding Emitter Positioning for Nanoflow Electrospray Ionization with a High-Capacity Inlet Capillary | Journal of the American Society for Mass Spectrometry pubs.acs.org/doi/10.1021/...

Quantifying the ∼75–95% of Peptides in DIA-MS Data Sets that Were Not Previously Quantified We have developed a novel algorithm termed GoldenHaystack (GH) that was designed for enhanced peptide quantification of data-independent acquisition liquid-mass spectrometry (DIA-LC-MS) data files reg...

dx.doi.org/10.1021/acs....

A Novel Compact Multi-Reflecting Time-of-Flight Mass Spectrometer Mass spectrometry is an indispensable tool for the rapid and in-depth analysis of complex mixtures across diverse biologically important fields including metabolomics, lipidomics, and proteomics. Thes...

pubs.acs.org/doi/10.1021/...

Characterization and Manipulation of Ion Clouds Inside an FT-ICR Instrument: A Laser Tomography Perspective The efficiency of many tandem mass spectrometry (MS/MS) techniques depends on the position of the trapped ion cloud and its overlap with a beam of photons or electrons. Here, we report photoactivated ...

pubs.acs.org/doi/10.1021/...

Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics 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 ...

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A Systematic Approach to Selecting the Right Tool for Mass Spectrometry Data Analysis in Protein and Peptide Bioanalysis 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...

analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...

Native Charge Detection Mass Spectrometry of Kilobase-Scale Messenger RNAs 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...

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High performance interface for boosting ion transmission in native mass spectrometry and beyond. 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...

dx.doi.org/10.26434/che...

Accessing Higher Order Mathieu Space Stability Zones to Narrow Isolation Widths Using Digital Quadrupole Time-of-Flight Mass Spectrometry 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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a close up of a man in a suit and tie with a question mark on his neck . ALT: a close up of a man in a suit and tie with a question mark on his neck .

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Feedback Control for Electrospray Ionization Based on The Shape of The Liquid Meniscus at The ESI Emitter Stable electrospray ionization is crucial for ensuring consistent ion generation in mass spectrometry. Previously, a feedback control system based on …

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Feedback Control for Electrospray Ionization Based on The Shape of The Liquid Meniscus at The ESI Emitter Stable electrospray ionization is crucial for ensuring consistent ion generation in mass spectrometry. Previously, a feedback control system based on …

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Characterization of Gas-Phase Native(-like) Proteins Using Structures for Lossless Ion Manipulations 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...

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My contribution to the family Christmas sugar cookie designs #teammassspec

There has recently been another flare up of people bashing quads and saying we should replace them with mobility analysis. I still have a hard time with this argument. The quad has plenty of utility in an instrument with high res mobility. If nothing else it can knock out unwanted charge states.

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS 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.

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Application of a Gradient-Threaded Discrete Twisted Dipole Ion Guide (GTDIG) for High-Efficiency Ion Propulsion and an Expanded m/z Bandwidth in Mass Spectrometry 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 ...

dx.doi.org/10.1021/jasm...

High‐Resolution Ion Mobility as an Alternative to Quadrupole‐Based Precursor Isolation for Reducing Chimeric Fragmentation Spectra in Bottom‐Up Proteomics analyticalsciencejou...

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#proteomics #prot-paper

What's Happening At the Water Surface Anyway?

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Theoretical Study Synchronized Reverse Scan Collision-Induced Dissociation in Digital Linear Ion Trap 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...

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Comparison of the results of the aberration approach for the calculation of electrostatic TOF mass analyzers with simulation in SIMION In the last few years, high-resolution time-of-flight mass analyzers (TOF-MA) have been intensively developed. Their development requires tools that p…

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A Radio Frequency Ion Guide for Transporting Cooled Ions Through Differential Vacuum Stages: Design and Simulation 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 ...

dx.doi.org/10.1021/jasm...

This has been my exact experience/impression of AI tools in science

Physics and Physicists: ChatGPT and Gemini Can't Do Real Physics Research physicsandphysicists.blogspot.com/2025/11/chat...

Multistage Tandem Mass Spectrometry Using an Electron-Activated Dissociation Device with a Linear Ion Trap and Structural Identification of Cardiolipins 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...

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Characterization of Mobility-Dependent Ion Confinement in Rotating Electric Fields 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...

pubs.acs.org/doi/10.1021/...