ArticleScientific data2020
A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS.
Article in Scientific data, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Proteomic Evidence for Biofilm-Mediated Copper Stress Adaptation in Oleidesulfovibrio alaskensis G20.Environmental microbiology · 2026Article
- Dear-OMG: An Omics-General Compression Method for Genomics, Proteomics and Metabolomics Data.Interdisciplinary sciences, computational life sciences · 2026Article
- A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs.Scientific data · 2026Article
- TheJournal of proteome research · 2026Article
- Bacterial Proteomics and Antibiotic Resistance Identification: Is Single-Cell Analysis a Worthwhile Pursuit?Pathogens (Basel, Switzerland) · 2025Review
- Proteomic Insights into IgA Nephropathy: A Comprehensive Analysis of Differentially Expressed Proteins in the Kidney.ACS omega · 2025Article
- A reference database enabling in-depth proteome and PTM analysis of mouse immune cells.Scientific data · 2025Article
- Dereplication of secondary metabolites from Sophora flavescens using an LC-MS/MS-based molecular networking strategy.Scientific reports · 2025Article
- A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism.Nature communications · 2025Article
- SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics.Interdisciplinary sciences, computational life sciences · 2024Article
- The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences.Nucleic acids research · 2024Article
- Proteome profiling of Campylobacter jejuni 81-176 at 37 °C and 42 °C by label-free mass spectrometry.BMC microbiology · 2024Article
- A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS.Scientific data · 2023Article
- Toward Single Bacterium Proteomics.Journal of the American Society for Mass Spectrometry · 2023Article
- DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.Patterns (New York, N.Y.) · 2023Article
- Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer.Journal of proteome research · 2023Article
- A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics.Cell reports methods · 2023Article
- Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics.Communications biology · 2023Article
- A method to enrich polypeptidyl-tRNAs to capture snapshots of translation in the cell.Nucleic acids research · 2023Article
- Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
9 authors.
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Abstract
Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries that are generally derived from a priori measurements of peptides for each species. Although Escherichia coli (E. coli) is among the best studied model organisms, so far there is no spectral assay library for the bacterium publicly available. Here, we generated a spectral assay library for 4,014 of the 4,389 annotated E. coli proteins using one- and two-dimensional fractionated samples, and ion mobility separation enabling deep proteome coverage. We demonstrate the utility of this high-quality library with robustness in quantitation of the E. coli proteome and with rapid-chromatography to enhance throughput by targeted DIA-MS. The spectral assay library supports the detection and quantification of 91.5% of all E. coli proteins at high-confidence with 56,182 proteotypic peptides, making it a valuable resource for the scientific community. Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28).
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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.