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

Nature Methods
Alvaro Sebastian Vaca JacomeJ. D. Jaffe

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.

References

Apr 2, 2005·Analytical Chemistry·Jeffrey C SilvaScott Geromanos
Jan 10, 2006·Molecular & Cellular Proteomics : MCP·Jeffrey C SilvaScott J Geromanos
Jul 4, 2009·Analytical Chemistry·Alexandre PanchaudDavid R Goodlett
Jul 9, 2010·Molecular & Cellular Proteomics : MCP·Tamar GeigerMatthias Mann
Apr 27, 2012·Molecular & Cellular Proteomics : MCP·Hannes RöstRuedi Aebersold
Nov 28, 2013·Mass Spectrometry Reviews·John D ChapmanChristophe D Masselon
Apr 15, 2014·Nature Biotechnology·Hannes L RöstRuedi Aebersold
Jan 20, 2015·Nature Methods·Chih-Chiang TsouAlexey I Nesvizhskii
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
May 23, 2015·Nature Protocols·Jarrett D EgertsonMichael J MacCoss
Aug 27, 2016·Journal of the American Society for Mass Spectrometry·Jacob D JaffeD R Mani
Nov 1, 2016·Nature Biotechnology·Pedro NavarroStefan Tenzer

❮ Previous
Next ❯

Citations

May 1, 2021·Journal of Clinical Medicine·Rintaro SaitoToru Takebayashi
Jul 10, 2021·Nature Biotechnology·Pavel SinitcynJürgen Cox
Jul 15, 2021·Journal of Proteome Research·Christoph Stingl, Theo M Luider
Aug 27, 2021·Scientific Data·Deborah O Dele-OniJacob D Jaffe

❮ Previous
Next ❯

Datasets Mentioned

BETA
PXD002952

Methods Mentioned

BETA
scraping

Software Mentioned

Linux RedHat6
Spectrum Mill
Percolator
garde
Avant
Skyline
EncyclopeDIA
SWATHProphet
OpenSWATH
Windows

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

BioRxiv : the Preprint Server for Biology
Alvaro Sebastian Vaca JacomeJ. D. Jaffe
Emerging Infectious Diseases
Polyxeni Potter
Krankenpflege. Soins infirmiers
F Taillens
Annals of Translational Medicine
Tu D Dan, Joshua D Palmer
© 2021 Meta ULC. All rights reserved