The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology

Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.

nature.com

Identification of E3 ligase substrates and PROTAC-induced ubiquitylation sites using proximity-based identification of ubiquitin sites (PrIUS) - Communications Biology

Proximity-dependent biotinylation coupled with ubiquitin remnant enrichment identifies PROTAC-induced ubiquitylation sites and E3 ligase substrates.

dlvr.it

Chemical Metabolomics: Chemical Biology Tools for Advanced Metabolism Investigations

The human metabolism has been investigated for several millennia. The metabolome is known for a high complexity due to a large number of different metabolites that are present at different concentrations. Metabolomics has been developed as a field to investigate the entire human metabolome and to elucidate disease development mechanisms. This Minireview compiles and discusses the Chemical Biology tools in the past decades developed for advanced metabolomics investigations. ABSTRACT Human metabolism has been investigated to understand disease onset for the discovery of new selective pharmaceuticals and the development of diagnostics for early disease detection. Metabolomics, as an interdisciplinary research field, has been implemented to investigate the entirety of the complex metabolite profiles predominantly using mass spectrometry. In the past two decades, the development of chemical biology tools for the detailed metabolism investigation has received a boost to advance metabolomics analyses. Especially, the identification of the microbiome and its importance for human physiology were the main motivation for these strategies. These new tools at the intersection of Chemistry and Biology have especially aided to uncover previously unknown metabolites in humans and have slowly elucidated metabolites produced by microbial communities. These Chemical Biology tools, integrated with metabolomics tools and technologies, build the foundation for Chemical Metabolomics investigations, which have led to the discovery of important metabolites that are modulators or readouts for disease development and human homeostasis. This overview article focuses on the recent developments and the diversity of Chemical Biology tools and technologies, particularly methods involving chemoselective probes, in vivo analysis, host-microbiome co-metabolism, and activity metabolomics, in the context of understanding human metabolism at the molecular level.

dlvr.it

Blood proteomics: insights from public data - Genome Biology

The circulating blood proteome comprises soluble and cellular components that reflect physiological and pathological states across tissues. Advances in mass spectrometry and affinity-based proteomics ...

link.springer.com

Faces of Mass Spectrometry

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Improving the Quadrupole to Ion Mobility Region in a Digital Quadrupole/Ion Mobility/Orbitrap Mass Spectrometer

A quadrupole/drift tube ion mobility/Orbitrap instrument requires pumping from atmosphere to 10–5 Torr in the quadrupole analyzer region, back to 1 Torr for the drift tube, and a return to 10–5 Torr for the Orbitrap high vacuum region. The Orbitrap high vacuum region contains the transfer multipole, C-trap, and HCD cell. Insufficient pumping between the drift tube and quadrupole leads to helium in the quadrupole analyzer chamber which compromises performance. Additional vacuum regions were added between the drift tube and the analyzer chamber to maintain the analyzer pressure below 5.5 × 10–5 Torr with the drift tube pressurized to 1.5 Torr of He. In this configuration, the isolation of a single charge state of C-reactive protein (m/z 5,000) was demonstrated. Fourier transform ion mobility spectra were acquired with the quadrupole in full scan mode and in the isolation mode. Ion optic voltages were optimized for both helium and nitrogen bath gases in the drift tube so that minimal ion heating was observed entering the drift tube. These instrument modifications enable improved ion transfer efficiency, allowing for better ion isolation by the digital quadrupole ion mobility separation of large protein complexes, as illustrated by the 23+ and 24+ charge states of C-reactive protein.

pubs.acs.org

a man in a space suit is looking at a screen that says mission day

ALT: a man in a space suit is looking at a screen that says mission day

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SCIEX summit 2025 - a live virtual event

Hear from industry experts about the latest advancements in mass spectrometry

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Retrospective metabolomics via dual-dimensional deconvolution using ZT Scan DIA 2.0

Herein, we present a scanning data-independent acquisition (DIA) approach (ZT Scan DIA 2.0) combined with dual-dimensional tandem mass spectrometry spectral deconvolution along both the quadrupole and...

biorxiv.org

Ep183: Sabah Oney on CAR-T Cells Against Solid Tumors

Podcast Episode · The Long Run with Luke Timmerman · 08/06/2025 · 56m

podcasts.apple.com

Assistant/Associate/Professor for Biological and Physical Chemistry

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Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling - Nature Communications

To improve annotation in non-targeted metabolomics studies, authors develop a Multiplexed Chemical Metabolomics (MCheM) platform, combining post-column derivatization with integrated data processing. ...

nature.com

pubs.acs.org

OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data

The Bruker timsTOF Pro is an instrument that couples trapped ion mobility spectrometry (TIMS) to high-resolution time-of-flight (TOF) mass spectrometry (MS). For proteomics, lipidomics, and metabolomics applications, the instrument is typically interfaced with a liquid chromatography (LC) system. The resulting LC-TIMS-MS data sets are, in general, several gigabytes in size and are stored in the proprietary Bruker Tims data format (TDF). The raw data can be accessed using proprietary binaries in C, C++, and Python on Windows and Linux operating systems. Here we introduce a suite of computer programs for data accession, including OpenTIMS, TimsR, and TimsPy. OpenTIMS is a C++ library capable of reading Bruker TDF files. It opens up Bruker’s proprietary codebase. TimsPy and TimsR build on top of OpenTIMS, enabling swift and user-friendly data access to the raw data with Python and R. Both programs are available under a GPL3 license on all major platforms, extending the possibility to interact with timsTOF data to macOS. Additionally, OpenTIMS is capable of translating Bruker data into HDF5 files that can be easily analyzed from Python with the vaex module. OpenTIMS and TimsPy therefore provide easy and quick access to Bruker timsTOF raw data.

pubs.acs.org