Search Results - "MacLean BX"

Koina: Democratizing machine learning for proteomics research.

Authors: Lautenbacher L Yang KL Kockmann T et al.

Source: Nature communications [Nat Commun] 2025 Nov 11; Vol. 16 (1), pp. 9933. Date of Electronic Publication: 2025 Nov 11.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.

Authors: Wen B Hsu C Shteynberg D et al.

Source: Nature communications [Nat Commun] 2025 Nov 06; Vol. 16 (1), pp. 9815. Date of Electronic Publication: 2025 Nov 06.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

ToxBase: A Multidimensional ToxCast Reference Database for High-Throughput Human Exposome Analysis.

Authors: Nguyen R Rangel G Liu X et al.

Source: Environmental science & technology [Environ Sci Technol] 2026 Jun 23; Vol. 60 (24), pp. 17314-17327. Date of Electronic Publication: 2026 Jun 09.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 0213155 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5851 (Electronic) Linking ISSN: 0013936X NLM ISO Abbreviation: Environ Sci Technol Subsets: MEDLINE

Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics.

Authors: Wen B Paez JS Hsu C et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Mar 31. Date of Electronic Publication: 2026 Mar 31.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Development of Highly Multiplex Targeted Proteomics Assays in Biofluids Using a Nominal Mass Ion Trap Mass Spectrometer.

Authors: Plubell DL Remes PM Wu CC et al.

Source: Molecular & cellular proteomics : MCP [Mol Cell Proteomics] 2026 Feb; Vol. 25 (2), pp. 101506. Date of Electronic Publication: 2026 Jan 07.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Inc. on behalf of American Society for Biochemistry and Molecular Biology Country of Publication: United States NLM ID: 101125647 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-9484 (Electronic) Linking ISSN: 15359476 NLM ISO Abbreviation: Mol Cell Proteomics Subsets: MEDLINE

Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists.

Authors: Hsu C Shulman N Stewart HI et al.

Source: Journal of proteome research [J Proteome Res] 2025 Nov 07; Vol. 24 (11), pp. 5742-5754. Date of Electronic Publication: 2025 Oct 22.

Publication Type: Journal Article; Evaluation Study

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.

Authors: Wen B Hsu C Shteynberg D et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Aug 04. Date of Electronic Publication: 2025 Aug 04.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics - Beyond identification lists.

Authors: Hsu C Shulman N Stewart H et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Jul 30. Date of Electronic Publication: 2025 Jul 30.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching.

Authors: Timmins-Schiffman EB Khanna R Brown T et al.

Source: Journal of proteome research [J Proteome Res] 2025 Mar 07; Vol. 24 (3), pp. 1317-1328. Date of Electronic Publication: 2025 Feb 25.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.

Authors: Remes PM Jacob CC Heil LR et al.

Source: Journal of proteome research [J Proteome Res] 2024 Dec 06; Vol. 23 (12), pp. 5476-5486. Date of Electronic Publication: 2024 Oct 30.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

A Framework for Quality Control in Quantitative Proteomics.

Authors: Tsantilas KA Merrihew GE Robbins JE et al.

Source: Journal of proteome research [J Proteome Res] 2024 Oct 04; Vol. 23 (10), pp. 4392-4408. Date of Electronic Publication: 2024 Sep 09.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

A framework for quality control in quantitative proteomics.

Authors: Tsantilas KA Merrihew GE Robbins JE et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2024 Aug 11. Date of Electronic Publication: 2024 Aug 11.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer.

Authors: Plubell DL Remes PM Wu CC et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 11. Date of Electronic Publication: 2024 Jun 11.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Hybrid Quadrupole Mass Filter - Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.

Authors: Remes PM Jacob CC Heil LR et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 01. Date of Electronic Publication: 2024 Jun 01.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.

Authors: Rojas Echeverri JC Hause F Iacobucci C et al.

Source: Analytical chemistry [Anal Chem] 2024 May 14; Vol. 96 (19), pp. 7373-7379. Date of Electronic Publication: 2024 May 02.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 0370536 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-6882 (Electronic) Linking ISSN: 00032700 NLM ISO Abbreviation: Anal Chem Subsets: MEDLINE

Audit logs to enforce document integrity in Skyline and Panorama.

Authors: Rohde T Chupalov R Shulman N et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2020 Aug 01; Vol. 36 (15), pp. 4366-4368.

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition.

Authors: Heil LR Damoc E Arrey TN et al.

Source: Journal of proteome research [J Proteome Res] 2023 Oct 06; Vol. 22 (10), pp. 3290-3300. Date of Electronic Publication: 2023 Sep 08.

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition.

Authors: Heil LR Damoc E Arrey TN et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2023 Aug 07. Date of Electronic Publication: 2023 Aug 07.

Publication Type: Preprint; Journal Article

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Targeted proteomics data interpretation with DeepMRM.

Authors: Park J Wilkins C Avtonomov D et al.

Source: Cell reports methods [Cell Rep Methods] 2023 Jul 11; Vol. 3 (7), pp. 100521. Date of Electronic Publication: 2023 Jul 11 (Print Publication: 2023).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Elsevier Inc Country of Publication: United States NLM ID: 9918227360606676 Publication Model: eCollection Cited Medium: Internet ISSN: 2667-2375 (Electronic) Linking ISSN: 26672375 NLM ISO Abbreviation: Cell Rep Methods Subsets: MEDLINE

MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale.

Authors: Kohler D Staniak M Tsai TH et al.

Source: Journal of proteome research [J Proteome Res] 2023 May 05; Vol. 22 (5), pp. 1466-1482. Date of Electronic Publication: 2023 Apr 05.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE