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.

scholarly journals A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

2019 ◽  
Author(s):  
Dorte B. Bekker-Jensen ◽  
Ana Martínez del Val ◽  
Sophia Steigerwald ◽  
Patrick Rüther ◽  
Kyle Fort ◽  
...  
Keyword(s):  
Mass Spectrometer ◽  
Ion Mobility ◽  
Rat Tissues ◽  
Label Free ◽  
Mass Spectrometers ◽  
Proteome Coverage ◽  
Data Independent Acquisition ◽  
Orbitrap Mass Spectrometer ◽  
Peptide Precursors ◽  
Free Quantification

ABSTRACTState-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 unique peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 minute LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.

scholarly journals A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements

2018 ◽  
Vol 17 (10) ◽  
pp. 2051-2067 ◽  
Author(s):  
Sibylle Pfammatter ◽  
Eric Bonneil ◽  
Francis P. McManus ◽  
Satendra Prasad ◽  
Derek J. Bailey ◽  
...  
Keyword(s):  
Ion Mobility ◽  
Proteome Coverage ◽  
Mobility Device

scholarly journals A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

2020 ◽  
Vol 19 (4) ◽  
pp. 716-729 ◽  
Author(s):  
Dorte B. Bekker-Jensen ◽  
Ana Martínez-Val ◽  
Sophia Steigerwald ◽  
Patrick Rüther ◽  
Kyle L. Fort ◽  
...  
Keyword(s):  
Mass Spectrometer ◽  
Ion Mobility ◽  
Rat Tissues ◽  
Label Free ◽  
Mass Spectrometers ◽  
Proteome Coverage ◽  
Data Independent Acquisition ◽  
Orbitrap Mass Spectrometer ◽  
Peptide Precursors ◽  
Free Quantification

State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 min LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument, we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.

Electron Microscopy in Molecular Biology

1967 ◽  
Vol 25 ◽  
pp. 2-3
Author(s):  
Cecil E. Hall
Keyword(s):  
Electron Microscopy ◽  
Molecular Biology ◽  
Noise Level ◽  
Molecular Structures ◽  
Material Structure ◽  
The Arts ◽  
Shadow Casting ◽  
Electron Image ◽  
High Degree ◽  
Very High

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.

A Low-Noise, High-Gain Quasi-Millimeter-Wave Receiver MMIC with a Very High Degree of Integration Using 3D-MMIC Technology

2011 ◽  
Vol E94-C (10) ◽  
pp. 1548-1556 ◽  
Author(s):  
Takana KAHO ◽  
Yo YAMAGUCHI ◽  
Kazuhiro UEHARA ◽  
Kiyomichi ARAKI
Keyword(s):  
Millimeter Wave ◽  
High Gain ◽  
Low Noise ◽  
High Degree ◽  
Very High ◽  
Millimeter Wave Receiver

scholarly journals Multi-Locus Selection and the Structure of Variation at the white Gene of Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 635-645 ◽  
Author(s):  
David A Kirby ◽  
Wolfgang Stephan
Keyword(s):  
Drosophila Melanogaster ◽  
White Gene ◽  
Transcriptional Unit ◽  
North American Population ◽  
Evolutionary Mechanisms ◽  
Locus Selection ◽  
Neutral Equilibrium ◽  
History Of ◽  
High Degree ◽  
Very High

Abstract We surveyed sequence variation and divergence for the entire 5972-bp transcriptional unit of the white gene in 15 lines of Drosophila melanogaster and one line of D. simulans. We found a very high degree of haplotypic structuring for the polymorphisms in the 3′ half of the gene, as opposed to the polymorphisms in the 5′ half. To determine the evolutionary mechanisms responsible for this pattern, we sequenced a 1612-bp segment of the white gene from an additional 33 lines of D. melanogaster from a European and a North American population. This 1612-bp segment encompasses an 834bp region of the white gene in which the polymorphisms form high frequency haplotypes that cannot be explained by a neutral equilibrium model of molecular evolution. The small number of recombinants in the 834bp region suggests epistatic selection as the cause of the haplotypic structuring, while an investigation of nucleotide diversity supports a directional selection hypothesis. A multi-locus selection model that combines features from both-hypotheses and takes the recent history of D. melanogaster into account may be the best explanation for these data.

scholarly journals The Antibacterial Effects of Resin-Based Dental Sealants: A Systematic Review of In Vitro Studies

Materials ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 413
Author(s):  
Saad Saeed AlShahrani ◽  
Mana’a Saleh AlAbbas ◽  
Isadora Martini Garcia ◽  
Maha Ibrahim AlGhannam ◽  
Muath Abdulrahman AlRuwaili ◽  
...  
Keyword(s):  
Antibacterial Agents ◽  
Data Extraction ◽  
Risk Of Bias ◽  
Dental Sealants ◽  
Medium Risk ◽  
Metabolic Activities ◽  
High Degree ◽  
Phosphate Buffered Saline ◽  
Full Text Screening

This review aimed to assess the antimicrobial effects of different antibacterial agents/compounds incorporated in resin-based dental sealants. Four databases (PubMed, MEDLINE, Web of Science and Scopus) were searched. From the 8052 records retrieved, 275 records were considered eligible for full-text screening. Nineteen studies met the inclusion criteria. Data extraction and quality assessment was performed by two independent reviewers. Six of the nineteen included studies were judged to have low risk of bias, and the rest had medium risk of bias. Compounds and particles such as zinc, tin, Selenium, chitosan, chlorhexidine, fluoride and methyl methacrylate were found to be effective in reducing the colony-forming unit counts, producing inhibition zones, reducing the optical density, reducing the metabolic activities, reducing the lactic acid and polysaccharide production and neutralizing the pH when they are added to the resin-based dental sealants. In addition, some studies showed that the antibacterial effect was not significantly different after 2 weeks, 2 months and 6 months aging in distilled water or phosphate-buffered saline. In conclusion, studies have confirmed the effectiveness of adding antibacterial agents/compounds to dental sealants. However, we should consider that these results are based on laboratory studies with a high degree of heterogeneity.

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