Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.

التفاصيل البيبلوغرافية
العنوان:	Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.
المؤلفون:	Ammar C; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany., Schessner JP; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany., Willems S; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany., Michaelis AC; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany., Mann M; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany. Electronic address: mmann@biochem.mpg.de.
المصدر:	Molecular & cellular proteomics : MCP [Mol Cell Proteomics] 2023 Jul; Vol. 22 (7), pp. 100581. Date of Electronic Publication: 2023 May 22.
نوع المنشور:	Journal Article; Research Support, Non-U.S. Gov't
اللغة:	English
بيانات الدورية:	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
أسماء مطبوعة:	Publication: 2021- : [New York, NY] : Elsevier Inc. on behalf of American Society for Biochemistry and Molecular Biology Original Publication: Bethesda, MD : American Society for Biochemistry and Molecular Biology, [2002-
مواضيع طبية MeSH:	Proteome/analysis , Proteomics/methods, Ecosystem ; Peptides/analysis ; Mass Spectrometry/methods ; Software
مستخلص:	Recent advances in mass spectrometry-based proteomics enable the acquisition of increasingly large datasets within relatively short times, which exposes bottlenecks in the bioinformatics pipeline. Although peptide identification is already scalable, most label-free quantification (LFQ) algorithms scale quadratic or cubic with the sample numbers, which may even preclude the analysis of large-scale data. Here we introduce directLFQ, a ratio-based approach for sample normalization and the calculation of protein intensities. It estimates quantities via aligning samples and ion traces by shifting them on top of each other in logarithmic space. Importantly, directLFQ scales linearly with the number of samples, allowing analyses of large studies to finish in minutes instead of days or months. We quantify 10,000 proteomes in 10 min and 100,000 proteomes in less than 2 h, a 1000-fold faster than some implementations of the popular LFQ algorithm MaxLFQ. In-depth characterization of directLFQ reveals excellent normalization properties and benchmark results, comparing favorably to MaxLFQ for both data-dependent acquisition and data-independent acquisition. In addition, directLFQ provides normalized peptide intensity estimates for peptide-level comparisons. It is an important part of an overall quantitative proteomic pipeline that also needs to include high sensitive statistical analysis leading to proteoform resolution. Available as an open-source Python package and a graphical user interface with a one-click installer, it can be used in the AlphaPept ecosystem as well as downstream of most common computational proteomics pipelines. Competing Interests: Conflict of interest The authors declare no competing interests. (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
فهرسة مساهمة:	Keywords: algorithms; label-free; protein intensity; proteomics; quantification
المشرفين على المادة:	0 (Proteome) 0 (Peptides)
تواريخ الأحداث:	Date Created: 20230524 Date Completed: 20230724 Latest Revision: 20230726
رمز التحديث:	20240628
مُعرف محوري في PubMed:	PMC10315922
DOI:	10.1016/j.mcpro.2023.100581
PMID:	37225017
قاعدة البيانات:	MEDLINE

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تدمد:	1535-9484
DOI:	10.1016/j.mcpro.2023.100581