ArticleMolecular & cellular proteomics : MCP2020
Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries.
Article in Molecular & cellular proteomics : MCP, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 167 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
167 citing papers in PubMed.
- Proteomic Profiling of Xenobiotic and Nutrient Transporters in Human Placenta of Different Gestational Ages.Clinical pharmacology and therapeutics · 2026Article
- Robotic handling preserves iPSC-derived vascular smooth muscle cell differentiation.Materials today. Bio · 2026Article
- Review
- Bypassing Androgens: Retina-Targeted 17β-Estradiol Delivery via DHED Eye Drops Ameliorates Orchiectomy-Induced Shifts in the Male Rat Visual Cortex Proteome.Antioxidants (Basel, Switzerland) · 2026Article
- Development and Validation of a Streamlined Workflow for Proteomic Analysis of Proteins and Post-translational Modifications from Dried Blood.Journal of proteome research · 2026Article
- Proteomic profiling of xenobiotic and nutrient transporters in human placenta of different gestational ages.bioRxiv : the preprint server for biology · 2026Article
- Comparative Evaluation of DDA- and DIA-Based Proteomic Workflows in Beryllium-Related Lung Disease.bioRxiv : the preprint server for biology · 2026Article
- Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition.bioRxiv : the preprint server for biology · 2026Article
- Consensus statement on mass spectrometry-based proteomic analysis of cardiac tissue.Nature cardiovascular research · 2026Article
- Limited Proteolysis Mass Spectrometry to Identify Protein Structural Differences in Brain Tissue.Bio-protocol · 2026Article
- Stress Granule Sequestration of CCR4-NOT Promotes Poly(A) Lengthening of Stress-Survival Transcripts.bioRxiv : the preprint server for biology · 2026Article
- Cytoplasmic localization of pseudouridine synthase 7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.Nature communications · 2026Article
- Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage.Nature methods · 2026Article
- Proteomic Profiling of Complement Components in Glomerular Disease.Laboratory investigation; a journal of technical methods and pathology · 2026Article
- Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies.bioRxiv : the preprint server for biology · 2026Article
- Mag-Net Strong Anion Exchange Enables Isolation of Ovarian Cancer Ascites Extracellular Vesicles for Proteomic Biomarker Discovery.Bio-protocol · 2026Article
- Proteomic profiling of human omental and subcutaneous adipose tissue in individuals with a broad range of BMI.Scientific data · 2026Article
- Extracellular matrix proteolysis maintains synapse plasticity during brain development.Nature neuroscience · 2026Article
- Is Protein Quantification and Physical Normalization Always Necessary in Proteomics?bioRxiv : the preprint server for biology · 2026Article
- Development of Highly Multiplex Targeted Proteomics Assays in Biofluids Using a Nominal Mass Ion Trap Mass Spectrometer.Molecular & cellular proteomics : MCP · 2026Article
107 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Data independent acquisition (DIA) is an attractive alternative to standard shotgun proteomics methods for quantitative experiments. However, most DIA methods require collecting exhaustive, sample-specific spectrum libraries with data dependent acquisition (DDA) to detect and quantify peptides. In addition to working with non-human samples, studies of splice junctions, sequence variants, or simply working with small sample yields can make developing DDA-based spectrum libraries impractical. Here we illustrate how to acquire, queue, and validate DIA data without spectrum libraries, and provide a workflow to efficiently generate DIA-only chromatogram libraries using gas-phase fractionation (GPF). We present best-practice methods for collecting DIA data using Orbitrap-based instruments and develop an understanding for why DIA using an Orbitrap mass spectrometer should be approached differently than when using time-of-flight instruments. Finally, we discuss several methods for analyzing DIA data without libraries.
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.