ArticleJournal of the American Society for Mass Spectrometry2019
Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition.
Article in Journal of the American Society for Mass Spectrometry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.Analytical chemistry · 2026Article
- Early-activated extracellular matrix proteins shape the metabolic and spatial dynamics of the kidney fibrotic microenvironment.Nature metabolism · 2026Article
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Article
- Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling.Nature communications · 2025Article
- Optimized Time-Segmented Acquisition Expands Peptide and Protein Identification in TIMS-TOF Pro Mass Spectrometry.Journal of proteome research · 2025Article
- An Extensive Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions.bioRxiv : the preprint server for biology · 2024Article
- Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.Nature communications · 2024Article
- Reciprocal antagonism of PIN1-APC/CNature communications · 2024Article
- EGFR targeting PhosTACs as a dual inhibitory approach reveals differential downstream signaling.Science advances · 2024Article
- Wnt5 controls splenic myelopoiesis and neutrophil functional ambivalency during DSS-induced colitis.Cell reports · 2024Article
- The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8Nature communications · 2024Article
- An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.Nature communications · 2023Article
- 7SK methylation by METTL3 promotes transcriptional activity.Science advances · 2023Article
- Coupling suspension trapping-based sample preparation and data-independent acquisition mass spectrometry for sensitive exosomal proteomic analysis.Analytical and bioanalytical chemistry · 2022Article
- DeepLC can predict retention times for peptides that carry as-yet unseen modifications.Nature methods · 2021Article
- Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes.Molecular omics · 2021Article
- BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples.Analytical chemistry · 2021Article
- Global and Site-Specific Effect of Phosphorylation on Protein Turnover.Developmental cell · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Due to the technical advances of mass spectrometers, particularly increased scanning speed and higher MS/MS resolution, the use of data-independent acquisition mass spectrometry (DIA-MS) became more popular, which enables high reproducibility in both proteomic identification and quantification. The current DIA-MS methods normally cover a wide mass range, with the aim to target and identify as many peptides and proteins as possible and therefore frequently generate MS/MS spectra of high complexity. In this report, we assessed the performance and benefits of using small windows with, e.g., 5-m/z width across the peptide elution time. We further devised a new DIA method named RTwinDIA that schedules the small isolation windows in different retention time blocks, taking advantage of the fact that larger peptides are normally eluting later in reversed phase chromatography. We assessed the direct proteomic identification by using shotgun database searching tools such as MaxQuant and pFind, and also Spectronaut with an external comprehensive spectral library of human proteins. We conclude that algorithms like pFind have potential in directly analyzing DIA data acquired with small windows, and that the instrumental time and DIA cycle time, if prioritized to be spent on small windows rather than on covering a broad mass range by large windows, will improve the direct proteome coverage for new biological samples and increase the quantitative precision. These results further provide perspectives for the future convergence between DDA and DIA on faster MS analyzers.
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