Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MSRescore with MSPIP timsTOF fragmentation prediction model.

Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we develop a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS).

Substrate profiling of the metalloproteinase ovastacin uncovers specific enzyme-substrate interactions and discloses fertilization-relevant substrates.

The metalloproteinase ovastacin is released by the mammalian egg upon fertilization and cleaves a distinct peptide bond in zona pellucida protein 2 (ZP2), a component of the enveloping extracellular matrix. This limited proteolysis causes zona pellucida hardening, abolishes sperm binding, and thereby regulates fertility. Accordingly, this process is tightly controlled by the plasma protein fetuin-B, an endogenous competitive inhibitor.

Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis.

The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro.

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).

IsoSpec2: Ultrafast Fine Structure Calculator.

High-resolution mass spectrometry becomes increasingly available with its ability to resolve the fine isotopic structure of measured analytes. It allows for high-sensitivity spectral deconvolution, leading to less false-positive identifications. Analytes can be identified by comparing their theoretical isotopic signal with the observed peaks.

Critical points of the three-dimensional Bose-Hubbard model from on-site atom number fluctuations.

We discuss how positions of critical points of the three-dimensional Bose-Hubbard model can be accurately obtained from variance of the on-site atom number operator, which can be experimentally measured. The idea that we explore is that the derivative of the variance, with respect to the parameter driving the transition, has a pronounced maximum close to critical points. We show that Quantum Monte Carlo studies of this maximum lead to precise determination of critical points for the superfluid-Mott insulator transition in systems with mean number of atoms per lattice site equal to one, two, and three.

Enhancing Sensitivity of Microflow-Based Bottom-Up Proteomics through Postcolumn Solvent Addition.

The introduction of more sensitive mass spectrometers allows researchers to adapt front-end liquid chromatography (LC) to individual needs for the analysis of complex proteomes. Where absolute sensitivity is not paramount, it is advantageous to switch from a highly sensitive nanoflow-LC setup, the de facto standard platform in mass-spectrometry (MS)-based discovery proteomics, to a more robust, high-throughput-compatible microflow or conventional-flow setup. To enhance the microflow-LC-MS electrospray process of complex proteomic samples, we tested the effects of different solvents, including 2-propanol, methanol, and acetonitrile, pure or as mixture with dimethyl sulfoxide, which were added postcolumn to the eluting sample.

masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry.

Top-down mass spectrometry methods are becoming continuously more popular in the effort to describe the proteome. They rely on the fragmentation of intact protein ions inside the mass spectrometer. Among the existing fragmentation methods, electron transfer dissociation is known for its precision and wide coverage of different cleavage sites.

Leaf and Plant Age Affects Photosynthetic Performance and Photoprotective Capacity.

In this work, we studied the changes in high-light tolerance and photosynthetic activity in leaves of the Arabidopsis () rosette throughout the vegetative stage of growth. We implemented an image-analysis work flow to analyze the capacity of both the whole plant and individual leaves to cope with excess excitation energy by following the changes in absorbed light energy partitioning. The data show that leaf and plant age are both important factors influencing the fate of excitation energy.

Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry.

Electron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several concurrent reactions triggered by the transfer of an electron from its anion source to sample cations. Transferring an electron causes peptide backbone cleavage while leaving labile post-translational modifications intact.

IsoSpec: Hyperfast Fine Structure Calculator.

As high-resolution mass spectrometry (HRMS) becomes increasingly available, the need of software tools capable of handling more complex data is surging. The complexity of the HRMS data stems partly from the presence of isotopes that give rise to more peaks to interpret compared to lower resolution instruments. However, a new generation of fine isotope calculators is on the rise.

Locating the quantum critical point of the Bose-Hubbard model through singularities of simple observables.

We show that the critical point of the two-dimensional Bose-Hubbard model can be easily found through studies of either on-site atom number fluctuations or the nearest-neighbor two-point correlation function (the expectation value of the tunnelling operator). Our strategy to locate the critical point is based on the observation that the derivatives of these observables with respect to the parameter that drives the superfluid-Mott insulator transition are singular at the critical point in the thermodynamic limit. Performing the quantum Monte Carlo simulations of the two-dimensional Bose-Hubbard model, we show that this technique leads to the accurate determination of the position of its critical point.

Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin.

Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions-primarily different forms of charge reduction-occur under ETD conditions, as evidenced by the distorted isotope patterns usually observed. In this work, we analyze these isotope patterns to compare the stability of nondissociative electron transfer (ETnoD) products, specifically noncovalent c/z fragment complexes, across a range of ubiquitin conformational states.

Tunneling-induced restoration of the degeneracy and the time-reversal symmetry breaking in optical lattices.

We study the ground-state properties of bosons loaded into the p band of a one-dimensional optical lattice. We show that the phase diagram of the system is substantially affected by the anharmonicity of the lattice potential. In particular, for a certain range of tunneling strength, the full many-body ground state of the system becomes degenerate.

Fast dynamics for atoms in optical lattices.

Cold atoms in optical lattices allow for accurate studies of many body dynamics. Rapid time-dependent modifications of optical lattice potentials may result in significant excitations in atomic systems. The dynamics in such a case is frequently quite incompletely described by standard applications of tight-binding models (such as, e.