Faculty Opinions recommendation of Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

2016 ◽  
Author(s):  
Alejandro Wolf-Yadlin
Keyword(s):  
Data Extraction ◽  
Proteome Analysis ◽  
Data Independent Acquisition

scholarly journals Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

2012 ◽  
Vol 11 (6) ◽  
pp. O111.016717 ◽  
Author(s):  
Ludovic C. Gillet ◽  
Pedro Navarro ◽  
Stephen Tate ◽  
Hannes Röst ◽  
Nathalie Selevsek ◽  
...  
Keyword(s):  
Data Extraction ◽  
Proteome Analysis ◽  
Data Independent Acquisition

scholarly journals Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition

2019 ◽  
Vol 18 (4) ◽  
pp. 760-772 ◽  
Author(s):  
Piotr Grabowski ◽  
Sebastian Hesse ◽  
Sebastian Hollizeck ◽  
Meino Rohlfs ◽  
Uta Behrends ◽  
...  
Keyword(s):  
Human Neutrophil ◽  
Proteome Analysis ◽  
Monogenic Disease ◽  
Neutrophil Granulocytes ◽  
Data Independent Acquisition ◽  
Using Data

Peptide Identification and Quantification by Gas Phase Fractionation Enables Proteomics Without Liquid Chromatography

2020 ◽  
Author(s):  
Jesse Meyer ◽  
Natalie M. Niemi ◽  
David J. Pagliarini ◽  
Joshua J. Coon
Keyword(s):  
Liquid Chromatography ◽  
Data Collection ◽  
Gas Phase ◽  
Biomarker Discovery ◽  
Proteome Analysis ◽  
Peptide Identification ◽  
Analysis Data ◽  
New Approach ◽  
Data Independent Acquisition ◽  
Cultured Human Cells

<p>Liquid chromatography mass spectrometry (LC-MS) delivers sensitive peptide analysis for proteomics, but the methodology requires extensive analysis time, hampering throughput. Here, we demonstrate that flow injection analysis data-independent acquisition (FIA-DIA), using gas-phase peptide separation instead of LC, offers extremely fast proteome analysis. Incorporating ion mobility with FIA-DIA, we demonstrate the targeted quantification of over 500 proteins within minutes of MS data collection (~3.5 proteins/second). We show the utility of this technology to perform a complex multifactorial proteome study of interactions between nutrients, genotype, and mitochondrial toxins in a collection of cultured human cells. More than 45,000 quantitative protein measurements from 132 samples were achieved in only 4.4 hours of MS data collection. Enabling fast, unbiased proteome quantification without LC, FIA-DIA offers a new approach to boosting throughput critical to drug and biomarker discovery studies that require analysis of thousands of proteomes.</p>

scholarly journals Recent Developments in Data Independent Acquisition (DIA) Mass Spectrometry: Application of Quantitative Analysis of the Brain Proteome

2020 ◽  
Vol 13 ◽  
Author(s):  
Ka Wan Li ◽  
Miguel A. Gonzalez-Lozano ◽  
Frank Koopmans ◽  
August B. Smit
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Quantitative Analysis ◽  
Brain Research ◽  
Proteome Analysis ◽  
Protein Isolate ◽  
Elution Time ◽  
Data Independent Acquisition ◽  
Peptide Precursor ◽  
Brain Proteome

Mass spectrometry is the driving force behind current brain proteome analysis. In a typical proteomics approach, a protein isolate is digested into tryptic peptides and then analyzed by liquid chromatography–mass spectrometry. The recent advancements in data independent acquisition (DIA) mass spectrometry provide higher sensitivity and protein coverage than the classic data dependent acquisition. DIA cycles through a pre-defined set of peptide precursor isolation windows stepping through 400–1,200 m/z across the whole liquid chromatography gradient. All peptides within an isolation window are fragmented simultaneously and detected by tandem mass spectrometry. Peptides are identified by matching the ion peaks in a mass spectrum to a spectral library that contains information of the peptide fragment ions' pattern and its chromatography elution time. Currently, there are several reports on DIA in brain research, in particular the quantitative analysis of cellular and synaptic proteomes to reveal the spatial and/or temporal changes of proteins that underlie neuronal plasticity and disease mechanisms. Protocols in DIA are continuously improving in both acquisition and data analysis. The depth of analysis is currently approaching proteome-wide coverage, while maintaining high reproducibility in a stable and standardisable MS environment. DIA can be positioned as the method of choice for routine proteome analysis in basic brain research and clinical applications.

scholarly journals Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

2019 ◽  
Author(s):  
Florian Meier ◽  
Andreas-David Brunner ◽  
Max Frank ◽  
Annie Ha ◽  
Isabell Bludau ◽  
...  
Keyword(s):  
Ion Mobility ◽  
Data Extraction ◽  
Ion Current ◽  
Proteome Coverage ◽  
Data Independent Acquisition ◽  
Quantitative Accuracy ◽  
Peptide Precursor ◽  
Mobility Device ◽  
High Degree ◽  
Very High

ABSTRACTData independent acquisition (DIA) modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions are sampled. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current. We extend an established targeted data extraction workflow by including the ion mobility dimension for both signal extraction and scoring, thereby increasing the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a very high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.

Peptide Identification and Quantification by Gas Phase Fractionation Enables Proteomics Without Liquid Chromatography

2020 ◽  
Author(s):  
Jesse Meyer ◽  
Natalie M. Niemi ◽  
David J. Pagliarini ◽  
Joshua J. Coon
Keyword(s):  
Liquid Chromatography ◽  
Data Collection ◽  
Gas Phase ◽  
Biomarker Discovery ◽  
Proteome Analysis ◽  
Peptide Identification ◽  
Analysis Data ◽  
New Approach ◽  
Data Independent Acquisition ◽  
Cultured Human Cells

<p>Liquid chromatography mass spectrometry (LC-MS) delivers sensitive peptide analysis for proteomics, but the methodology requires extensive analysis time, hampering throughput. Here, we demonstrate that flow injection analysis data-independent acquisition (FIA-DIA), using gas-phase peptide separation instead of LC, offers extremely fast proteome analysis. Incorporating ion mobility with FIA-DIA, we demonstrate the targeted quantification of over 500 proteins within minutes of MS data collection (~3.5 proteins/second). We show the utility of this technology to perform a complex multifactorial proteome study of interactions between nutrients, genotype, and mitochondrial toxins in a collection of cultured human cells. More than 45,000 quantitative protein measurements from 132 samples were achieved in only 4.4 hours of MS data collection. Enabling fast, unbiased proteome quantification without LC, FIA-DIA offers a new approach to boosting throughput critical to drug and biomarker discovery studies that require analysis of thousands of proteomes.</p>

scholarly journals Discovery of Candidate Stool Biomarker Proteins for Biliary Atresia Using Proteome Analysis by Data-Independent Acquisition Mass Spectrometry

Proteomes ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 36
Author(s):  
Eiichiro Watanabe ◽  
Yusuke Kawashima ◽  
Wataru Suda ◽  
Tomo Kakihara ◽  
Shinya Takazawa ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biliary Atresia ◽  
Early Stage ◽  
Proteome Analysis ◽  
Kasai Portoenterostomy ◽  
Protein Levels ◽  
Data Independent Acquisition ◽  
Pediatric Diseases ◽  
Prompt Diagnosis ◽  
Potential Biomarkers

Biliary atresia (BA) is a destructive inflammatory obliterative cholangiopathy of the neonate that affects various parts of the bile duct. If early diagnosis followed by Kasai portoenterostomy is not performed, progressive liver cirrhosis frequently leads to liver transplantation in the early stage of life. Therefore, prompt diagnosis is necessary for the rescue of BA patients. However, the prompt diagnosis of BA remains challenging because specific and reliable biomarkers for BA are currently unavailable. In this study, we discovered potential biomarkers for BA using deep proteome analysis by data-independent acquisition mass spectrometry (DIA–MS). Four patients with BA and three patients with neonatal cholestasis of other etiologies (non-BA) were recruited for stool proteome analysis. Among the 2110 host-derived proteins detected in their stools, 49 proteins were significantly higher in patients with BA and 54 proteins were significantly lower. These varying stool protein levels in infants with BA can provide potential biomarkers for BA. As demonstrated in this study, the deep proteome analysis of stools has great potential not only in detecting new stool biomarkers for BA but also in elucidating the pathophysiology of BA and other pediatric diseases, especially in the field of pediatric gastroenterology.

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