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Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire

ABSTRACT: Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Alexey I. Nesvizhskii

PROVIDER: MSV000080875 | MassIVE | Sat Apr 01 04:29:00 BST 2017

SECONDARY ACCESSION(S): PXD003179

REPOSITORIES: MassIVE

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Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.

Tsou Chih-Chiang CC Tsai Chia-Feng CF Teo Guo Ci GC Chen Yu-Ju YJ Nesvizhskii Alexey I AI

Proteomics 20160722 15-16

We describe an improved version of the data-independent acquisition (DIA) computational analysis tool DIA-Umpire, and show that it enables highly sensitive, untargeted, and direct (spectral library-free) analysis of DIA data obtained using the Orbitrap family of mass spectrometers. DIA-Umpire v2 implements an improved feature detection algorithm with two additional filters based on the isotope pattern and fractional peptide mass analysis. The targeted re-extraction step of DIA-Umpire is updated ...[more]

PMID: 27246681

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Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire

Project description:Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire

2016-06-16 | PXD003179 | Pride

Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM-DIA, and Untargeted DIA.

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Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.

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Data-independent Acquisition for the orbitrap. A tutorial.

Project description:Data-independent acquisition (DIA) is a powerful mass spectrometric technique to perform both protein identification and quantification of complex protein samples. Setting up DIA methods on Orbitrap analyzers requires a thorough overview over the actions the Orbitrap mass spectrometers carry out. This tutorial is written with the intention to give an overview over the important parameters to consider as well as which measurements to carry out to get the most out of your DIA method when setting it up on an Orbitrap mass analyzer. Instead of giving the optimal DIA settings, all steps in the construction and optimization of the DIA method are shown and discussed in a way that allow tailored DIA methods. Key steps are: building the spectral library after sample fractionation, decide upon the number of data points per chromatographic peak, determine scan times of each mass spectrometric step, construct various DIA methods using these data and evaluate their performance. This proposed DIA method development strategy was tested on digested lysates from Pseudomonas Aeruginosa and compared to conventional DDA analysis to put the DIA results in a perspective.

2019-08-09 | PXD011449 | JPOST Repository

Scanning quadrupole DIA - Scanning Quadrupole Data Independent Acquisition - Part A

Project description:A scanning quadrupole data independent acquisition (DIA) method is described and characterised for the qualitative and quantitative label free proteomic analysis of complex biological samples. The principle of the scanning quadrupole DIA is discussed and the effect of the optimization of analytical instrument characteristics, such as acquisition speed, sample complexity, and scan/integration time in relation to sample complexity for a number of different model proteomes of various complexity and dynamic range, including plasma, human cell lines, and bacteria samples, discussed. In addition, its technological merits from an acquisition neutral perspective are reviewed. The qualitative and semi-quantitative performance of the method is illustrated and contrasted for the analysis of a well-characterised human cell line sample using untargeted and targeted search strategies. The application of the method is demonstrated for the analysis of the calcineurin-dependent proteome of drug treated Aspergillus fumigatus. The design of these experiments afforded assessment of the precision and accuracy of scanning quadrupole data independent acquisition (DIA) method as will be demonstrated by peptide and protein centric analysis of the study pool QC samples of the study. Moreover, novel and specific interactors in response to drug treatment that are indicative of the role of calcineurin role in regulating these effectors have been identified.

2017-09-14 | PXD005869 | Pride

Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics.

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DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics

Project description:This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics", Nature Methods, in press Raw files are deposited here in ProteomeXchange and are associated with the DIA-Umpire processed data. All DIA-Umpire processed results for each sample together with DDA results are deposited in separated folders. Also see the "DataSampleID.xlsx" associated with this Readme file. Internal reference from the Gingras lab ProHits implementation: Project 94, Export version VS2 (Tsou_DIA-Umpire)

2015-01-21 | PXD001587 | Pride

Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications.

Project description: Not available

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Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments.

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DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

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