Dataset Information

Avant-garde: an automated data-driven DIA data curation tool.

ABSTRACT: Several challenges remain in data-independent acquisition (DIA) data analysis, such as to confidently identify peptides, define integration boundaries, remove interferences, and control false discovery rates. In practice, a visual inspection of the signals is still required, which is impractical with large datasets. We present Avant-garde as a tool to refine DIA (and parallel reaction monitoring) data. Avant-garde uses a novel data-driven scoring strategy: signals are refined by learning from the dataset itself, using all measurements in all samples to achieve the best optimization. We evaluate the performance of Avant-garde using benchmark DIA datasets and show that it can determine the quantitative suitability of a peptide peak, and reach the same levels of selectivity, accuracy, and reproducibility as manual validation. Avant-garde is complementary to existing DIA analysis engines and aims to establish a strong foundation for subsequent analysis of quantitative mass spectrometry data.

SUBMITTER: Vaca Jacome AS

PROVIDER: S-EPMC7723322 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Avant-garde: an automated data-driven DIA data curation tool.

Vaca Jacome Alvaro Sebastian AS Peckner Ryan R Shulman Nicholas N Krug Karsten K DeRuff Katherine C KC Officer Adam A Christianson Karen E KE MacLean Brendan B MacCoss Michael J MJ Carr Steven A SA Jaffe Jacob D JD

Nature methods 20201116 12

Several challenges remain in data-independent acquisition (DIA) data analysis, such as to confidently identify peptides, define integration boundaries, remove interferences, and control false discovery rates. In practice, a visual inspection of the signals is still required, which is impractical with large datasets. We present Avant-garde as a tool to refine DIA (and parallel reaction monitoring) data. Avant-garde uses a novel data-driven scoring strategy: signals are refined by learning from th ...[more]

PMID: 33199889

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Project description:Because food byproducts (waste) are rich in phytoconstituents, valorizing them is crucial for global food security. However, conventional extraction (CE), including decoction, maceration, Soxhlet, etc., for agro byproducts' polyphenol extraction are time-consuming and rely significantly on vast volumes of potentially aggressive solvents. Hence, Avantgarde extraction technologies, including non-thermal (high hydrostatic pressure (HHPE), pulsed-electric field (PEF), high voltage electrical discharges (HVED), etc.) and thermal extraction (supercritical fluid (SCF), subcritical water extraction (SWE), microwave-assisted extraction (MAE), etc.), as well as their thermal combinations (SCF-PLE, SCCO2-SWE, SCCO2-MAE, etc.), non-thermal combinations (HHPE + UAE, PEF + UAE, HVED + UAE, etc.) and combined thermalnon-thermal (MAE-UAE, etc.) are increasingly replacing CE. However, a review of combined Avant-garde extraction escalation technologies (non-thermal/thermal extraction matrix) for extracting polyphenols from agro-byproducts is limited. Hence, this manuscript reviewed Avant-garde extraction technologies (non-thermal/thermal extraction matrix) for extracting phenolics from agro-byproducts in the last 5 years. The key factors affecting polyphenols' extraction from the byproduct, the recent applications of Avant-garde technologies, and their principle were reviewed using databases from Web of Science and Lens.org. The results demonstrated that combined Avant-garde extraction escalation technologies increase extractability, resulting in polyphenols with higher extraction rates, fewer contaminants, and preservation of thermosensitive components. Therefore, combined Avant-garde extraction technologies should be explored over the next five years. Implementing an integrated process and the strategic sequencing of diverse Avant-garde extraction technologies are important. Thus, further investigation is required to explore the sequencing process and its potential impact on the extraction of phenolics from agro-byproducts.

Dataset Information

Avant-garde: an automated data-driven DIA data curation tool.

Publications

Avant-garde: an automated data-driven DIA data curation tool.

Similar Datasets

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