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Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results

Molecular & cellular proteomics, 2017-12, Vol.16 (12), p.2296-2309 [Peer Reviewed Journal]

2017 © 2017 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology. ;2017 by The American Society for Biochemistry and Molecular Biology, Inc. ;Copyright American Society for Biochemistry and Molecular Biology Dec 2017 ;2017 by The American Society for Biochemistry and Molecular Biology, Inc. 2017 The American Society for Biochemistry and Molecular Biology, Inc. ;ISSN: 1535-9476 ;EISSN: 1535-9484 ;DOI: 10.1074/mcp.RA117.000314 ;PMID: 29070702

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Title:
Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results
Author: Bruderer, Roland ; Bernhardt, Oliver M. ; Gandhi, Tejas ; Xuan, Yue ; Sondermann, Julia ; Schmidt, Manuela ; Gomez-Varela, David ; Reiter, Lukas
Subjects: Animals ; Cell Line ; Cell lines ; Chromatography, Liquid ; Coefficient of variation ; HEK293 Cells ; HeLa Cells ; Humans ; Mass spectrometry ; Mass spectroscopy ; Mice ; Optimization ; Peptides ; Peptides - analysis ; Peptides - genetics ; Proteins ; Proteomics ; Proteomics - methods ; Quadrupoles ; Reproducibility ; Reproducibility of Results ; Scientific imaging ; Sequence Analysis, Protein ; Somatosensory cortex ; Spectroscopy ; Synaptic strength ; Tandem Mass Spectrometry - methods ; Technological Innovation and Resources ; Tissues
Is Part Of: Molecular & cellular proteomics, 2017-12, Vol.16 (12), p.2296-2309
Description: Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we identified and quantified 6,383 proteins in human cell lines using 2-or-more peptides/protein and over 7100 proteins when including the 717 proteins that were identified on the basis of a single peptide sequence. 7739 proteins were identified in mouse tissues using 2-or-more peptides/protein and 8121 when including the 382 proteins that were identified based on a single peptide sequence. Missing values for proteins were within 0.3 to 2.1% and median coefficients of variation of 4.7 to 6.2% among technical triplicates. In very complex mixtures, we could quantify 10,780 proteins and 12,192 proteins when including the 1412 proteins that were identified based on a single peptide sequence. Using this optimized DIA, we investigated large-protein networks before and after the critical period for whisker experience-induced synaptic strength in the murine somatosensory cortex 1-barrel field. This work shows that parallel mass spectrometry enables proteome profiling for discovery with high coverage, reproducibility, precision and scalability.
Publisher: United States: Elsevier Inc
Language: English
Identifier: ISSN: 1535-9476
EISSN: 1535-9484
DOI: 10.1074/mcp.RA117.000314
PMID: 29070702
Source: GFMER Free Medical Journals
MEDLINE
PubMed Central
Alma/SFX Local Collection

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Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results

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