ArticleNature communications2025
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- A bivalent molecular glue linking lysine acetyltransferases to oncogene-induced cell death.Cell · 2026Article
- Differential lipid selectivity of StARD phospholipid transporters revealed by native MS.Nature communications · 2026Article
- Identification of the plant mitochondrial OrfX protein: A mass spectrometry approach.FEBS letters · 2026Article
- Targeted quantification assays for DNA repair and handling proteins and interactions in Huntington's disease models.bioRxiv : the preprint server for biology · 2026Article
- SLC16A6 is a tyrosine transporter for the melanosome.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule imaging reveals RNA polymerase II dynamics and TAF1-dependent promoter-proximal pause release.Nature communications · 2026Article
- The molecular basis for nuclear pore destruction by a proximity-inducing molecular glue.Cell chemical biology · 2026Article
- Spatial Single-Cell Proteomics Reveals Molecular Trajectories Of Tangle-Bearing Neurons In Alzheimer's Disease.bioRxiv : the preprint server for biology · 2026Article
- Orientia tsutsugamushi targets lamin A using Ank effectors and alters chromatin to inhibit NF-κB.Communications biology · 2026Article
- What Does Next-Generation Mass Spectrometry Offer for Proteomics? A Comprehensive Platform Comparison.Journal of proteome research · 2026Article
- Mutations outside the MR1 antigen binding groove differentially inhibit presentation of exogenous antigens.The Journal of biological chemistry · 2026Article
- Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.Nature communications · 2026Article
- iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.Genome biology · 2026Article
- xTracer: Integrating chromatogram and mobiligram correlations for untargeted peptide identification in SLIM-based PAMAF data.bioRxiv : the preprint server for biology · 2026Article
- Sensitive detection of cancer antigens enabled by user-defined peptide libraries.Nature biotechnology · 2026Article
- A Preliminary Predictive Panel for Pre-Frailty Based on Serum Proteomic Biomarkers: A Two-Phase Cross-Sectional Study.Clinical interventions in aging · 2026Article
- Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes.Journal of proteome research · 2025Article
- Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex.Cancer discovery · 2025Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
Corrections and comments
- Update of
Authors and funding
5 authors.
Funding
Abstract
Data-independent acquisition has become a widely used strategy for peptide and protein quantification in liquid chromatography-tandem mass spectrometry-based proteomics studies. The integration of ion mobility separation into data-independent acquisition analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using data-independent acquisition. We introduce diaTracer, a spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (mass to charge ratio, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved "pseudo-tandem mass spectra", facilitating direct ("spectral-library free") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from triple-negative breast cancer, cerebrospinal fluid, and plasma samples, data from phosphoproteomics and human leukocyte antigens immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass-offset searches.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.