ArticleJournal of the American Society for Mass Spectrometry2014
Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics.
Article in Journal of the American Society for Mass Spectrometry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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Who cites it
21 citing papers in PubMed, 44 citations in OpenAlex.
- Article
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- Proteomic Technology.Advances in experimental medicine and biology · 2026Review
- Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists.Journal of proteome research · 2025Article
- Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics - Beyond identification lists.bioRxiv : the preprint server for biology · 2025Article
- Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.Journal of proteome research · 2025Article
- Rapid assay development for low input targeted proteomics using a versatile linear ion trap.Nature communications · 2025Article
- LiLA: lipid lung-based ATLAS built through a comprehensive workflow designed for an accurate lipid annotation.Communications biology · 2024Article
- Comparative assessment and novel strategy on methods for imputing proteomics data.Scientific reports · 2022Article
- Mass-Spectrometry-Based Functional Proteomic and Phosphoproteomic Technologies and Their Application for Analyzing Ex Vivo and In Vitro Models of Hypertrophic Cardiomyopathy.International journal of molecular sciences · 2021Review
- Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives.International journal of molecular sciences · 2020Review
- Comparison of data acquisition modes with Orbitrap high-resolution mass spectrometry for targeted and non-targeted residue screening in aquacultured eel.Rapid communications in mass spectrometry : RCM · 2020Article
- Site-specific N-glycosylation of HeLa cell glycoproteins.Scientific reports · 2019Article
- Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.Journal of the American Society for Mass Spectrometry · 2019Article
- Rapid Food Product Analysis by Surface Acoustic Wave Nebulization Coupled Mass Spectrometry.Food analytical methods · 2018Article
- Maillard Proteomics: Opening New Pages.International journal of molecular sciences · 2017Review
- DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs.BMC bioinformatics · 2017Article
- Propafenone suppresses esophageal cancer proliferation through inducing mitochondrial dysfunction.American journal of cancer research · 2017Article
- Ion Activation Methods for Peptides and Proteins.Analytical chemistry · 2016Review
- mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.Journal of proteomics · 2015Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
Abstract
The most common data collection in shotgun proteomics is via data-dependent acquisition (DDA), a process driven by an automated instrument control routine that directs MS/MS acquisition from the highest abundant signals to the lowest. An alternative to DDA is data-independent acquisition (DIA), a process in which a specified range in m/z is fragmented without regard to prioritization of a precursor ion or its relative abundance in the mass spectrum, thus potentially offering a more comprehensive analysis of peptides than DDA. In this work, we evaluate both DDA and DIA on three different linear ion trap instruments: an LTQ, an LTQ modified with an electrodynamic ion funnel, and an LTQ Velos. These instruments represent both older (LTQ) and newer (LTQ Velos) ion trap designs (i.e., linear versus dual ion traps, respectively), and allow direct comparison of peptide identifications using both DDA and DIA analysis. Further, as the LTQ Velos has an enhanced "S-lens" ion guide to improve ion flux, we found it logical to determine if the former LTQ model could be leveraged by improving sensitivity by modifying with an electrodynamic ion guide of significantly different design to the S-lens. We find that the ion funnel enabled LTQ identifies more proteins in the insoluble fraction of a yeast lysate than the other two instruments in DIA mode, whereas the faster scanning LTQ Velos performs better in DDA mode. We explore reasons for these results, including differences in scan speed, source ion optics, and linear ion trap design.
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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.