ArticleJournal of proteome research2022
Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes.
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search.Nature communications · 2025Article
- The Enzyme Effect: Broadening the Horizon of MS Optimization to Nontryptic Digestion in Proteomics.Journal of the American Society for Mass Spectrometry · 2025Article
- IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.Journal of the American Society for Mass Spectrometry · 2024Article
- MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search.bioRxiv : the preprint server for biology · 2024Article
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.bioRxiv : the preprint server for biology · 2024Article
- Global detection of human variants and isoforms by deep proteome sequencing.Nature biotechnology · 2023Article
- ProtView: A Versatile Tool forJournal of proteome research · 2023Article
- Overview and considerations in bottom-up proteomics.The Analyst · 2023Review
- Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics.International journal of molecular sciences · 2022Review
- Addressing the Protease Bias in Quantitative Proteomics.Journal of proteome research · 2022Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
The use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments; however, due to the additional analysis time required, it has not been widely adopted in routine data-dependent acquisition (DDA) proteomic workflows. Alternatively, data-independent acquisition (DIA) has the potential to analyze multiplexed samples from different protease digests, but has been primarily optimized for fragmenting tryptic peptides. Here we evaluate a DIA multiplexing approach that combines three proteolytic digests (Trypsin, AspN, and GluC) into a single sample. We first optimize data acquisition conditions for each protease individually with both the canonical DIA fragmentation mode (beam type CID), as well as resonance excitation CID, to determine optimal consensus conditions across proteases. Next, we demonstrate that application of these conditions to a protease-multiplexed sample of human peptides results in similar protein identifications and quantitative performance as compared to trypsin alone, but enables up to a 63% increase in peptide detections, and a 45% increase in nonredundant amino acid detections. Nontryptic peptides enabled noncanonical protein isoform determination and resulted in 100% sequence coverage for numerous proteins, suggesting the utility of this approach in applications where sequence coverage is critical, such as protein isoform analysis.
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