Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis.

Optimizing data-independent acquisition methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here, we describe a real-time full mass range implementation of the phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals.

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth of protein quantification, especially for proteins and modifications of biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus increasing proteome depth.

Isolated Rh atoms in dehydrogenation catalysis.

Isolated active sites have great potential to be highly efficient and stable in heterogeneous catalysis, while enabling low costs due to the low transition metal content. Herein, we present results on the synthesis, first catalytic trials, and characterization of the GaRh phase and the hitherto not-studied GaRh phase. We used XRD and TEM for structural characterization, and with XPS, EDX we accessed the chemical composition and electronic structure of the intermetallic compounds.

Preparation of geometrically highly controlled Ga particle arrays on quasi-planar nanostructured surfaces as a SCALMS model system.

This study establishes a preparative route towards a model system for supported catalytically active liquid metal solutions (SCALMS) on nanostructured substrates. This model is characterized by a uniquely precise geometrical control of the gallium particle size distribution. In a SCALMS system, the Ga serves as a matrix material which can be decorated with a catalytically active material subsequently.

MaxDIA enables library-based and library-free data-independent acquisition proteomics.

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries.

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides.

Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. Although achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on prescheduled mass-to-charge and retention time windows.

EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification.

We developed EASI-tag (easily abstractable sulfoxide-based isobaric-tag), a new type of amine-derivatizing and sulfoxide-containing isobaric labeling reagents for highly accurate quantitative proteomics analysis using mass spectrometry. We observed that EASI-tag labels dissociate at low collision energy and generate peptide-coupled, interference-free reporter ions with high yield. Efficient isolation of C precursors and quantification at the MS2 level allowed accurate determination of quantitative differences between up to six multiplexed samples.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water.

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA).

Simulated Solute Tempering in Fully Polarizable Hybrid QM/MM Molecular Dynamics Simulations.

We successfully apply a solute tempering approach, which substantially reduces the large number of temperature rungs required in conventional tempering methods by solvent charge scaling, to hybrid molecular dynamics simulations combining quantum mechanics with molecular mechanics (QM/MM). Specifically, we integrate a combination of density functional theory (DFT) and polarizable MM (PMM) force fields into the simulated solute tempering (SST) concept. We show that the required DFT/PMM-SST weight parameters can be obtained from inexpensive calculations and that for alanine dipeptide (DFT) in PMM water three rungs suffice to cover the temperature range from 300 to 550 K.

Spectroscopic polarizable force field for amide groups in polypeptides.

The infrared spectra of polypeptides are dominated by the so-called amide bands. These bands originate from the electrostatically coupled vibrations of the strongly polar amide groups (AGs) making up the polypeptide backbone. Because the AGs are highly polarizable, external electric fields can shift the frequencies of the amide normal modes over wide spectral ranges.