Parallel Accumulation with Mobility Aligned Fragmentation (PAMAF) achieves near complete ion utilization and high spectral specificity by fragmenting all mobility separated precursors without quadrupole isolation. Leveraging the ultrahigh mobility resolution of SLIM, this quadrupole free strategy maximizes ion utilization efficiency and offers a promising approach in mass spectrometry based proteomics, particularly for low abundance peptides or low input samples. However, the unique data structure of PAMAF where precursor fragment relationships are encoded along the mobility dimension renders it incompatible with existing peptide identification tools. Here, we present xTracer, the first untargeted peptide identification algorithm developed specifically for PAMAF data. xTracer integrates correlations across both chromatographic and mobility dimensions to associate precursor and fragment ions, reconstruct pseudo-spectra, and enable database searching using well established DDA search engines. Applied to datasets with varying sample loads and acquisition throughputs, xTracer consistently achieved robust and reproducible peptide identifications, outperforming single domain correlation strategies. Overall, xTracer provides a versatile and high efficiency computational framework for reconstructing pseudo spectra from quadrupole free, mobility aligned fragmentation data, enhancing the analytical power of high resolution ion mobility (HRIM) based proteomics.

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Join us at the Keystone Symposia on B Cell and Antibody Responses, February 2027, in London, with field leaders!

“Groundbreaking” study uncovers why adenovirus-based shots caused life-threatening blood clots and bleeding in some people

In this study, an imaging technology, “VISUN,” is developed that allows live-cell visualization of unmodified influenza virus during infection with single-vRNP resolution. Combining VISUN with multipl...

To understand how proteins function, we need to know their three-dimensional structure. We use two techniques to determine such 3D structures of proteins and their complexes: X-ray crystallography and...

FEBS Advanced Lecture Course

Infectieziekte: Een breed werkende antistof in een neusspray beschermt tegen veel verschillende griepvirussen. Dat kan een belangrijk wapen worden bij een nieuwe pandemie.

Snell et al. develop sequencing methodology to identify full-length spike haplotypes and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence, accelerating viral evolution an...