#JASMS

Kermit Murray

@kkmurray.bsky.social

20 hours ago

[ASAP] A Miniature Ion Trap Particle Mass Spectrometer with an Integrated Optical and Charge Detection System Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00399

(JASMS) [ASAP] A Miniature Ion Trap Particle Mass Spectrometer with an Integrated Optical and Charge Detection System: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00399 (RSS) #MassSpecRSS #JASMS

@jasms.bsky.social

1 day ago

Selected as #ACS Editors’ Choice and free for a limited time!

This #JASMS paper demonstrates how HCD MS can distinguish O-GlcNAc from the Tn antigen in cancer cells, advancing glycoproteomics research.

Read it while it’s free: https://pubs.acs.org/doi/10.1021/jasms.5c00378

BioMassSpec

@realbiomassspec.bsky.social

2 days ago

A Computational Model for Determining Labeling Duration in Protein Turnover Studies Using a Single Deuterated Water Labeled Sample The time course of metabolic labeling using deuterated water, followed by liquid chromatography coupled with mass spectrometry, is employed to investigate the turnover rates of individual proteins in vivo. These labeling experiments are resource intensive. Computational methods that can determine turnover rates from a single and labeled for a short duration sample will help reduce these demands. We evaluated linear and logarithmic models to estimate protein turnover rates based on two samples (one nonlabeled and one labeled). Key factors such as the number of exchangeable hydrogens, body water enrichment in deuterium, protein turnover rate, and necessary changes in monoisotopic relative abundance established a range of labeling durations for the two-sample approach. We provide two inequalities that formally define this range of labeling duration for each peptide, which is integrated into an R Shiny App. We applied this two-sample approach to four murine tissues. By adjusting the labeling duration according to the turnover of the tissue proteome, the two-sample approach was able to analyze over 60% (1221 murine liver proteins) of the proteome previously assessed using a multisample approach.

A Computational Model for Determining Labeling Duration in Protein Turnover Studies Using a Single Deuterated Water Labeled Sample #JASMS pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

2 days ago

Faces of Mass Spectrometry/Chris Crittenden

Faces of Mass Spectrometry/Chris Crittenden #JASMS pubs.acs.org/doi/10.1021/...

Kermit Murray

@kkmurray.bsky.social

3 days ago

[ASAP] Faces of Mass Spectrometry/Chris Crittenden Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00074

(JASMS) [ASAP] Faces of Mass Spectrometry/Chris Crittenden: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00074 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

3 days ago

[ASAP] A Computational Model for Determining Labeling Duration in Protein Turnover Studies Using a Single Deuterated Water Labeled Sample Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00278

(JASMS) [ASAP] A Computational Model for Determining Labeling Duration in Protein Turnover Studies Using a Single Deuterated Water Labeled Sample: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00278 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

3 days ago

[ASAP] Discrimination of Threonine Isomers by Multiple-Stage Tandem Mass Spectrometry with Collision-Induced Dissociation Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00013

(JASMS) [ASAP] Discrimination of Threonine Isomers by Multiple-Stage Tandem Mass Spectrometry with Collision-Induced Dissociation: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00013 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

4 days ago

[ASAP] Data-Independent Acquisition (DIA) Strategy for Measuring Protein Stability Using Stability of Proteins from Rates of Oxidation (SPROX) Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00316

(JASMS) [ASAP] Data-Independent Acquisition (DIA) Strategy for Measuring Protein Stability Using Stability of Proteins from Rates of Oxidation (SPROX): Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00316 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

5 days ago

[ASAP] Direct Observation of Metastable Fragment Ions in Ultraviolet Photodissociation of Ubiquitin Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00432

(JASMS) [ASAP] Direct Observation of Metastable Fragment Ions in Ultraviolet Photodissociation of Ubiquitin: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00432 (RSS) #MassSpecRSS #JASMS

BioMassSpec

@realbiomassspec.bsky.social

5 days ago

Data-Independent Acquisition (DIA) Strategy for Measuring Protein Stability Using Stability of Proteins from Rates of Oxidation (SPROX) The stability of proteins from the rates of oxidation (SPROX) technique is a mass spectrometry-based approach for making protein folding stability measurements on the proteomic scale. The development and application of SPROX, to date, have primarily relied on the use of quantitative bottom-up proteomics and data-dependent acquisition (DDA) strategies using isobaric mass tags. Use of isobaric mass tags is attractive, as it enables the mass spectrometry readout in SPROX to be highly multiplexed. However, the use of such isobaric mass tags is restricted to DDA strategies, which can be limited in their proteomic coverage compared with data-independent acquisition (DIA) strategies. Reported here is a new “one-pot” SPROX workflow that employs a DIA readout and a label-free quantification strategy. Analysis of the proteins in an E. coli cell lysate using the DIA-SPROX strategy allowed for the calculation of transition midpoints with reasonable accuracy. The proteins from a S. cerevisiae cell lysate were also assessed for ligand-induced changes in their transition midpoints upon the introduction of cyclosporine A (CsA) to identify the protein targets of this well-studied ligand. The DIA-SPROX strategy developed here successfully identified known protein targets of CsA with a low false positive rate using a combination of two different software, Spectronaut and DIA-NN, for DIA data processing. We also find that the proteomic coverage obtained using DIA-SPROX is comparable to the coverage obtained in conventional DDA-SPROX experiments. Significantly, this comparable coverage can be achieved without a fractionation strategy (e.g., methionine-containing peptide enrichment) in DIA-SPROX.

Data-Independent Acquisition (DIA) Strategy for Measuring Protein Stability Using Stability of Proteins from Rates of Oxidation (SPROX) #JASMS pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

5 days ago

Direct Observation of Metastable Fragment Ions in Ultraviolet Photodissociation of Ubiquitin Ultraviolet photodissociation (UVPD) of proteins is known to exhibit conformation-dependent fragmentation patterns, but direct structural evidence linking precursor protein and fragment ions has been limited. Here, we apply tandem trapped-ion mobility spectrometry/tandem-mass spectrometry to compare collision cross sections of UVPD fragment ions generated from distinct conformers of ubiquitin. Under the high-pressure (∼4 mbar) and low-photon density (∼10 μJ laser pulse energies) conditions employed here, UVPD produces predominantly [b + 2] and [y – 2] ions at proline residues, consistent with direct bond cleavage from the electronically excited state. Our data show that these ions can retain a clear structural relationship to the precursor conformation: UVPD of compact, native-like ubiquitin yields fragments with collision cross sections ∼20% smaller than the corresponding ions produced from extended precursors or by collision-induced dissociation. Further, these compact UVPD fragments are kinetically trapped in metastable conformations, with substantial barriers preventing relaxation toward energetically favored gas-phase structures. We attribute this behavior to limited vibrational energy deposition per absorbed 213 nm photon combined with rapid collisional cooling, which suppress cumulative thermal activation and disfavor statistical fragmentation pathways, leaving direct excited-state dissociation as the dominant observable process. Together with prior UVPD studies on holo-myoglobin, our results suggest that UVPD fragments can retain aspects of their precursor tertiary structure.

Direct Observation of Metastable Fragment Ions in Ultraviolet Photodissociation of Ubiquitin #JASMS pubs.acs.org/doi/10.1021/...

@jasms.bsky.social

6 days ago

Call for Papers: Security & Forensic MS

#JASMS seeks submissions for a Special Issue aligned with the 2025 ASMS Asilomar theme. Topics include drug profiling, source attribution, IRMS, ambient ionization, and explosives analysis.

Deadline: 4/30/36
https://bit.ly/46Ur5Nk

ASMS

@asms.org

6 days ago

Call for Papers: Security & Forensic MS

#JASMS seeks submissions for a Special Issue aligned with the 2025 ASMS Asilomar theme. Topics include drug profiling, source attribution, IRMS, ambient ionization, and explosives analysis.

Deadline: 4/30/36
https://bit.ly/46Ur5Nk

Kermit Murray

@kkmurray.bsky.social

6 days ago

[ASAP] Optimization of Radially Segmented Ion Mirrors for High Resolution Charge Detection Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00337

(JASMS) [ASAP] Optimization of Radially Segmented Ion Mirrors for High Resolution Charge Detection Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00337 (RSS) #MassSpecRSS #JASMS

BioMassSpec

@realbiomassspec.bsky.social

6 days ago

Optimization of Radially Segmented Ion Mirrors for High Resolution Charge Detection Mass Spectrometry Charge detection mass spectrometry (CD-MS) enables mass measurements to be made for heterogeneous samples into the gigadalton regime. In CD-MS, ions are trapped in an electrostatic linear ion trap (ELIT) where they oscillate back and forth through a detection cylinder. The m/z is determined from the oscillation frequency, and the charge is obtained from the signal amplitude. The charge can be measured with a precision of better than 0.2 e (elementary charges), where ions can be assigned to the correct charge state with a low error rate. Thus, the main factor limiting mass resolution in CD-MS measurements is the imprecision in the m/z determination for individual ions. In prior work, it was shown that m/z resolving powers >300,000 could be achieved by optimizing the ELIT design to minimize the dependence of the ion’s oscillation frequency on the ion’s kinetic energy and trajectory. However, the high-resolution ELIT designs that we found were intolerant to small misalignments of the trap electrodes that result from manufacturing imprecision. A misalignment of less than 20 μm caused the trapping efficiency to drop to zero. The best resolving power achieved with a more tolerant ELIT design (where manufacturing imprecision does not catastrophically reduce the trapping efficiency) is 14,000–15,000. Here, we explore a solution to the intolerant ELIT designs where some of the ELIT mirror electrodes are segmented to allow small trim potentials to correct for mechanical misalignments. The trim potentials can be optimized under computer control to maximize trapping efficiency and m/z resolution. Trajectory simulations indicate that a high trapping efficiency can be recovered (>90%) while retaining high resolving powers (>200,000).

Optimization of Radially Segmented Ion Mirrors for High Resolution Charge Detection Mass Spectrometry #JASMS pubs.acs.org/doi/10.1021/...

Kermit Murray

@kkmurray.bsky.social

1 week ago

[ASAP] Oligomer-Dependent Gas-Phase Dissociation Behavior of 2-Butanone Peroxide (MEKP) Cations Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00450

(JASMS) [ASAP] Oligomer-Dependent Gas-Phase Dissociation Behavior of 2-Butanone Peroxide (MEKP) Cations: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00450 (RSS) #MassSpecRSS #JASMS

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Oligomer-Dependent Gas-Phase Dissociation Behavior of 2-Butanone Peroxide (MEKP) Cations 2-Butanone peroxide is a commonly used cross-linker in the chemical industry and a homemade explosive encountered by the forensic community. In this study, the dissociation behavior of ammonium cation...

Oligomer-Dependent Gas-Phase Dissociation Behavior of 2-Butanone Peroxide (MEKP) Cations #JASMS pubs.acs.org/doi/10.1021/...

Kermit Murray

@kkmurray.bsky.social

1 week ago

[ASAP] Integrating Ion Beam Control into a Commercial Platform for Improved Multimodal SIMS/MALDI Imaging Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00423

(JASMS) [ASAP] Integrating Ion Beam Control into a Commercial Platform for Improved Multimodal SIMS/MALDI Imaging: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00423 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

1 week ago

[ASAP] Interpretable Machine Learning to Decipher Myelodysplastic Syndrome-Associated Alterations of the Extracellular Matrix by Time-of-Flight Secondary Ion Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00343

(JASMS) [ASAP] Interpretable Machine Learning to Decipher Myelodysplastic Syndrome-Associated Alterations of the Extracellular Matrix by Time-of-Flight Secondary Ion Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00343 (RSS) #MassSpecRSS #JASMS

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Integrating Ion Beam Control into a Commercial Platform for Improved Multimodal SIMS/MALDI Imaging Mass spectrometry imaging (MSI) provides spatially resolved chemical analysis of surfaces and is widely applied in biological and biomedical research. Multimodal MSI can combine techniques such as secondary ion mass spectrometry (SIMS) and matrix-assisted laser desorption/ionization (MALDI) to leverage their complementary strengths. However, acquiring multimodal MSI data using separate instruments introduces challenges, including image coregistration and potential sample degradation during transfer. To address these limitations, we previously integrated a C60 ion gun into a prototype, commercially available MSI instrument, enabling SIMS, MALDI, and secondary electron imaging within a single platform. In this study, we implemented field of view (FoV) mode SIMS on this platform by rastering the ion beam, achieving an improved spatial resolution of 2 μm and surpassing the spatial resolution of the sample stage. Additionally, we optimized the instrument for elemental ion signals and observed enhanced sensitivity of selected species in SIMS through collision-induced dissociation (CID). To explore the usability of the ion gun for high-spatial-resolution image coregistration with other imaging modalities, fiducial markers were etched using the ion gun, creating a localized absence of signal in the etching locations, which can aid coregistration with optical imaging. Additionally, the secondary electrons produced by rastering the ion beam were used to image and assess the MALDI laser focus and power, allowing us to determine the optimal settings.

Integrating Ion Beam Control into a Commercial Platform for Improved Multimodal SIMS/MALDI Imaging #JASMS pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Interpretable Machine Learning to Decipher Myelodysplastic Syndrome-Associated Alterations of the Extracellular Matrix by Time-of-Flight Secondary Ion Mass Spectrometry Machine learning (ML) accelerates progress in many areas, including biomedical and clinical research. ML algorithms provide powerful options for efficiently analyzing multivariate data sets. We developed and validated an ML pipeline to detect myelodysplastic syndrome (MDS)-associated pathological alterations of extracellular matrices (ECMs) by time-of-flight secondary ion mass spectrometry (ToF-SIMS). A Bayesian-optimized neural network (NN) was trained and applied to classify ToF-SIMS spectra of ECM secreted by mesenchymal stromal cells (MSCs) derived from MDS patients and healthy reference donors. Validated by principal component analysis, the explainer tool SHapley Additive exPlanations (known as SHAP) was integrated into the analysis pipeline to unravel characteristic compositional and structural differences of the ECM variants. Our results demonstrate the potential of ToF-SIMS-ML for the label-free investigation of pathogenic alterations of the ECM. Integrated into the multiscale ECM analysis of cell and organoid-based disease models, the introduced methodology may facilitate advances in the development of novel diagnostic and therapeutic strategies.

Interpretable Machine Learning to Decipher Myelodysplastic Syndrome-Associated Alterations of the Extracellular Matrix by Time-of-Flight Secondary Ion Mass Spectrometry #JASMS pubs.acs.org/doi/10.1021/...

Kermit Murray

@kkmurray.bsky.social

1 week ago

[ASAP] Exploring Fluoroquinolone Protomer Populations Formed with MALDI and Plasma Post-Ionization Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00342

(JASMS) [ASAP] Exploring Fluoroquinolone Protomer Populations Formed with MALDI and Plasma Post-Ionization Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00342 (RSS) #MassSpecRSS #JASMS

@jasms.bsky.social

1 week ago

Hey, #TeamMassSpec! The latest edition of #JASMS is here. Read up on the latest: https://bit.ly/3KRQ4J8

#ASMS

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Exploring Fluoroquinolone Protomer Populations Formed with MALDI and Plasma Post-Ionization Mass Spectrometry Molecules that possess more than one protonation site can form protonation site isomers (protomers) in mass spectrometry. During the ionization process, a change in protonation site can alter the resulting collision-induced dissociation mass spectrum, which can hamper the accurate confirmation of unknown analytes in mass spectrometry workflows. In this study, we report the presence of protomers for ten fluoroquinolone antibiotics in a conventional matrix-assisted laser desorption ionization (MALDI) ion source and compare this against an atmospheric pressure MALDI plasma postionization (AP-MALDI-PPI) source. Irrespective of matrix composition, only the most stable protomer forms in a conventional MALDI ion source, which is consistent with a thermodynamically driven MALDI ionization process. In contrast, between 1–3 protomers form with an AP-MALDI-PPI source and this demonstrates that a different mechanism is responsible for analyte protonation. Protomer populations can be biased to favor the most stable protomer with high proton affinity MALDI matrices. Protomer populations can also be biased by doping the plasma with methanol or acetonitrile solvent vapor. Fluoroquinolone protomers are separated by trapped-ion mobility spectrometry (TIMS) and subjected to collision-induced dissociation. The protonation sites are assigned by the presence of unique fragment ions and comparing experimentally derived collisional cross sections TIMSCCSN2 against trajectory method CCSN2 calculations at the ωB97X-D/aug-cc-pVDZ//ωB97X-D/cc-pVDZ level of theory. This composite study shows that protomer population ratios change between MALDI and AP-MALDI-PPI ion sources, sample preparation method, and analyte structure, which can affect their ion mobility distributions and potentially impact their faithful confirmation.

Exploring Fluoroquinolone Protomer Populations Formed with MALDI and Plasma Post-Ionization Mass Spectrometry #JASMS pubs.acs.org/doi/10.1021/...

@jasms.bsky.social

2 weeks ago

What caught everyone’s eye this month? Here are our most-read #JASMS articles: the papers the mass spectrometry community couldn’t put down! Take a look: https://bit.ly/4pOfir4 #MassSpec #MassSpecCommunity

ASMS

@asms.org

2 weeks ago

What caught everyone’s eye this month? Here are the most-read #JASMS articles: the papers the mass spectrometry community couldn’t put down! Take a look: https://bit.ly/4pOfir4 #MassSpec #MassSpecCommunity

Kermit Murray

@kkmurray.bsky.social

2 weeks ago

[ASAP] Exploring the Potential of Ultrafast Arylation for Capping Cysteine Residues with Fixed Charge Modifications Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00400

(JASMS) [ASAP] Exploring the Potential of Ultrafast Arylation for Capping Cysteine Residues with Fixed Charge Modifications: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00400 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

2 weeks ago

[ASAP] Response Factor Correction for Quantitative Determination of Homooligomeric SsoSSB Binding to ssDNA by Native Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00446

(JASMS) [ASAP] Response Factor Correction for Quantitative Determination of Homooligomeric SsoSSB Binding to ssDNA by Native Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00446 (RSS) #MassSpecRSS #JASMS

Nick Riley

@nmriley.bsky.social

2 weeks ago

The mass range of tandem mass spectra can be categorized into three main regions. For glycopeptides, the lower mass range contains mainly oxonium ions, the middle range contains mainly peptide fragments, and the high range contains charge-reduced fragments. All regions contain valuable fragment ion information, but they can only be simultaneously accessed by breaking the 5–10–15 rule.

MS/MS scan range can be an afterthought that doesn't receive attention in method design, but improper settings can affect experimental outcomes. This is especially true in glycoproteomics.

A #glycotime thread about a new #JASMS paper on this idea from @riley-research.bsky.social

1/10

BioMassSpec

@realbiomassspec.bsky.social

2 weeks ago

Response Factor Correction for Quantitative Determination of Homooligomeric SsoSSB Binding to ssDNA by Native Mass Spectrometry Native mass spectrometry (nMS) has emerged as a complementary approach for elucidating molecular parameters of biological complexes relative to solution-phase experiments. Herein, we utilize nMS to determine the subunit binding affinities (Kd,i) of the single-stranded DNA binding protein (SSB) from Saccharolobus solfataricus (Sso) to poly dT single-stranded DNA (ssDNA) compared with the apparent Kd′ values obtained from solution-phase fluorescence anisotropy. This work resolves conflicting previous biochemical reports on the stoichiometry and affinities of SsoSSB while also highlighting the advantages and limitations of nMS quantification. Covalent concatemers of SsoSSB with increasing molecular weights were utilized as response factor (RF) standards to correct for physical and instrumental parameters that systematically underrepresent abundances from ionization of larger mass species. Furthermore, we show that regardless of the nMS quantification metric (peak area or intensity), meaningful comparative data can be extracted from multicomponent biochemical systems. Importantly, the binding affinities of the individual species (Kd,i) determined by nMS approach the apparent Kd′ from bulk solution-phase measurements but have the added benefit of separately quantifying individual binding steps within a multistep assembly process. Interestingly, the stoichiometries of SsoSSB binding to 15 or 30 nucleotides of ssDNA measured by nMS are subsaturating. The calculated binding affinities of the first and second SsoSSB molecules show some positive cooperativity, while the binding of the third is an order of magnitude weaker, suggesting that negative cooperativity is utilized to limit binding near the ends of the available length of the ssDNA.

Response Factor Correction for Quantitative Determination of Homooligomeric SsoSSB Binding to ssDNA by Native Mass Spectrometry #JASMS pubs.acs.org/doi/10.1021/...