ArticleScientific data2022
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Instrument-Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring Methods.Journal of proteome research · 2026Article
- Ground Truth-Based Evaluation of False Discovery Rate and Statistical Power in DIA Proteomics.bioRxiv : the preprint server for biology · 2026Article
- Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach.Journal of the American Society for Mass Spectrometry · 2026Article
- LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.Bioinformatics (Oxford, England) · 2025Article
- High-Throughput Label-free Single-Cell Proteomics Enabled by Multicolumn NanoLC with a 5-min Cycle Time.Research square · 2025Article
- Koina: Democratizing machine learning for proteomics research.Nature communications · 2025Article
- Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.Nature communications · 2025Article
- A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics.Analytical chemistry · 2025Article
- FastSpel: A Method for Fast Spectral Library Generation.Journal of proteome research · 2025Article
- Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set.Nature communications · 2025Article
- On the question of correct use of replicates in quantitative label-free proteomics.Analytical and bioanalytical chemistry · 2025Article
- Carafe enables high qualitybioRxiv : the preprint server for biology · 2025Article
- Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep.Analytical chemistry · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- TIMSJournal of proteome research · 2025Article
- A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities.Journal of proteome research · 2025Article
- Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition.Nature biotechnology · 2024Article
- Dear-PSM: A deep learning-based peptide search engine enables full database search for proteomics.Smart medicine · 2024Article
- A learned score function improves the power of mass spectrometry database search.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design. Therefore, we acquired a hybrid proteome mixture on different instrument platforms and in all currently available families of data acquisition. Here, we present a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset acquired using several of the most commonly used current day instrumental platforms. The dataset consists of over 700 LC-MS runs, including adequate replicates allowing robust statistics and covering over nearly 10 different data formats, including scanning quadrupole and ion mobility enabled acquisitions. Datasets are available via ProteomeXchange (PXD028735).
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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.