A5115600538- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Glycosylation and Glycoproteins Research
- Metabolomics and Mass Spectrometry Studies
- Analytical Chemistry and Chromatography
- Bacterial Genetics and Biotechnology
- Ubiquitin and proteasome pathways
- Monoclonal and Polyclonal Antibodies Research
- Carbohydrate Chemistry and Synthesis
- Mitochondrial Function and Pathology
- Plant nutrient uptake and metabolism
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Peptidase Inhibition and Analysis
- RNA modifications and cancer
- Pancreatic function and diabetes
- Receptor Mechanisms and Signaling
- Computational Drug Discovery Methods
- Protein purification and stability
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Nitric Oxide and Endothelin Effects
- Amino Acid Enzymes and Metabolism
- Ion-surface interactions and analysis
- Genomics and Phylogenetic Studies
Thermo Fisher Scientific (United States)
2016-2025
Thermo Fisher Scientific (Israel)
2011-2025
Massachusetts Institute of Technology
2023
University of Alberta
2023
King's College London
2016
British Heart Foundation
2016
St George's Hospital
2016
Universität Hamburg
2016
University Medical Center Hamburg-Eppendorf
2016
Thermo Fisher Scientific (Japan)
2011-2013
Although only a few years old, the combination of linear ion trap with an Orbitrap analyzer has become one standard mass spectrometers to characterize proteins and proteomes. Here we describe novel version this instrument family, Elite, which is improved in three main areas. The transfer optics path that blocks line sight achieve more robust operation. tandem MS acquisition speed dual cell now exceeds 12 Hz. Most importantly, resolving power been increased twofold for same transient length...
We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid acquisition strategy to sequence at both MS2 MS3 level new algorithmic design XlinkX v2.0 for analysis. As proof-of-concept we investigated proteome-wide interactions E. coli HeLa cell lysates, respectively, 1,158 3,301 unique ∼1% false discovery rate. interaction...
Abstract Knowledge of the subcellular distribution proteins is vital for understanding cellular mechanisms. Capturing proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning to niches low resolution and/or accuracy. Here we introduce hyperLOPIT, method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry multivariate data analysis. We apply hyperLOPIT pluripotent stem cell population whose...
Abstract Objective Enhanced lipid peroxidation is well established in traumatic brain injury. However, its molecular targets, identity of peroxidized phospholipid species, and their signaling role have not been deciphered. Methods Using controlled cortical impact as a model injury, we employed newly developed oxidative lipidomics approach to qualitatively quantitatively characterize the response. Results Electrospray ionization matrix‐assisted laser desorption/ionization mass spectrometry...
Mass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) challenged in effectively identifying the sites modification while simultaneously sequencing peptides. Here we tested hypothesis a combination high-energy C-trap dissociation (HCD) and electron transfer (ETD) could specifically target O-GlcNAc peptides elucidate amino acid sequence preserving attached GlcNAc residue for accurate site assignment. By taking advantage...
Abstract Antigen receptor signalling activates the canonical NF-κB pathway via CARD11/BCL10/MALT1 (CBM) signalosome involving key, yet ill-defined roles for linear ubiquitination. The paracaspase MALT1 cleaves and removes negative checkpoint proteins, amplifying lymphocyte responses in activation B-cell lymphoma subtypes. To identify new human substrates, we compare B cells from only known living mut/mut patient with healthy +/ mut family members using 10-plex Tandem Mass Tag TAILS...
Currently, glycans are attracting attention from the scientific community as potential biomarkers or posttranslational modifications (PTMs) of therapeutic proteins. However, structural characterization glycoproteins and glycopeptides remains analytically challenging. Here, we report on implementation a novel acquisition strategy termed higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation (HCD-PD-ETD) hybrid linear ion trap-orbitrap mass...
The number of publications in the field chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and probe protein-protein interactions has increased during last years. As technique is now becoming routine vitro vivo applications proteomics structural biology there a pressing need define protocols as well data analysis reporting formats. Such consensus formats should become accepted be shown lead reproducible...
S-Nitrosylation is a redox-based protein post-translational modification in response to nitric oxide signaling and involved wide range of biological processes. Detection quantification S-nitrosylation have been challenging tasks due instability low abundance the modification. Many studies used mass spectrometry (MS)-based methods with different thiol-reactive reagents label identify proteins S-nitrosylated cysteine (SNO-Cys). In this study, we developed novel iodoTMT switch assay (ISA) using...
Data dependent acquisition (DDA) of higher collision energy dissociation (HCD)-MS2 followed by electron transfer (ETD)-MS2 upon detection glycan-specific oxonium is one the better approaches in current LC-MS2 analysis intact glycopeptides. Although impressive numbers glycopeptide identification a direct database search have been reported, false positives remained high and difficult to determine. Even cases when peptide backbones were correctly identified, exact glycan moieties often...
Oxidative stress has been implicated in multiple human neurological and other disorders. Proteasomes are multi-subunit proteases critical for the removal of oxidatively damaged proteins. To understand stress-associated pathologies, it is important to uncover molecular events underlying regulation proteasomes upon oxidative stress. this end, we investigated H2O2 stress–induced changes 26S proteasome determined that stress-induced disassembly conserved from yeast human. Moreover, developed...
The SR Ca‐ATPase in skeletal muscle vesicles isolated from young adult (5 months) and aged (28 rats was analyzed for nitrotyrosine. Only the SERCA2a isoform contained significant amounts with approximately one four nitrotyrosine residues per old Ca‐ATPase, respectively. vitro exposure of to peroxynitrite yielded selective nitration even presence excess SERCA1a. No observed during nitric oxide O 2 . These data suggest vivo muscle. greater content tissue imolies an age‐associated increase...
Previous proteomics studies have partially unraveled the complexity of endothelial protein secretion but not investigated glycosylation, a key modification secreted and membrane proteins for cell communication. In this study, human umbilical vein cells were kept in serum-free medium before activation by phorbol-12-myristate-13 acetate, commonly used secretagogue that induces exocytosis vesicles. addition to 123 proteins, secretome was particularly rich proteins. Glycopeptides enriched...
Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species various types. The majority native MS experiments reported to-date has been conducted using direct infusion purified analytes into spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap spectrometers commercial sheathless interface enable high-performance separation, identification, structural characterization limited...
Cross-linking mass spectrometry (XL-MS) represents a recently popularized hybrid methodology for defining protein–protein interactions (PPIs) and analyzing structures of large protein assemblies. In particular, XL-MS strategies have been demonstrated to be effective in elucidating molecular details PPIs at the peptide resolution, providing complementary set structural data that can utilized refine existing complex or direct de novo modeling unknown structures. To study interaction dynamics...
Abstract Cross‐linking mass spectrometry (XL‐MS) is an attractive method for the proteome‐wide characterization of protein structures and interactions. Currently, depth in vivo XL‐MS studies lagging behind established applications to cell lysates, because cross‐linking reagents that can penetrate intact cells strategies enrich cross‐linked peptides lack efficiency. To tackle these limitations, we have developed a phosphonate‐containing cross‐linker, tBu‐PhoX, efficiently permeates various...
Adeno-associated viruses (AAVs) are non-enveloped ssDNA icosahedral T = 1 used as vectors for clinical gene delivery. Currently, there over 200 AAV-related trials and six approved biologics on the market. As such new analytical methods continually being developed to characterize monitor quality purity of manufactured AAV vectors, these include ion-exchange chromatography Direct Mass Technology. However, require homogeneous standards with a high molecular weight standard comparable mass an...
Monoclonal antibodies (mAbs) and antibody–drug conjugates (ADCs) are two of the most important therapeutic drug classes that require extensive characterization, whereas their large size structural complexity make them challenging to characterize demand use advanced analytical methods. Top-down mass spectrometry (TD-MS) is an emerging technique minimizes sample preparation preserves endogenous post-translational modifications (PTMs); however, TD-MS proteins suffers from low fragmentation...
Abstract We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS 2 ) that supports the acquisition of peptide fragment ions alongside their precursors. The approach enables true auto-curation HX data by mining rich set deuterated fragments, generated collisional-induced dissociation (CID), simultaneously confirm ID and authenticate MS 1 -based deuteration calculations. high redundancy provided fragments confidence assessment deuterium calculations using...
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype major facilitator superfamily transporters. With conformation-selective nanobody, we determined low-sugar affinity inward-facing Na + -bound cryoEM structure. available outward-facing sugar-bound showed that N- C-terminal residues inner barrier contribute...
A MALDI source is interfaced to a modified LTQ Orbitrap XL instrument. This work gives insight into the design and shows results obtained with coupled an accurate mass, high-resolution hybrid mass spectrometer. MALDI-produced ions fragment thereof produced in spectrometer may be analyzed detected by analyzer at maximum resolution of 100,000 (FWHM) m/z 400 high accuracy. An accuracy ≤2 ppm achieved internal calibration using lock functionality; external calibration, ≤3 routinely obtained....