scholarly journals Data-independent acquisition mass spectrometry enables reproducible characterization of microbiota function

2018 ◽  
Author(s):  
Juhani Aakko ◽  
Sami Pietilä ◽  
Tomi Suomi ◽  
Mehrad Mahmoudian ◽  
Raine Toivonen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dynamic Range ◽  
Functional Characterization ◽  
Research Area ◽  
Microbial Composition ◽  
Complex Samples ◽  
Data Independent Acquisition ◽  
Novel Approach ◽  
Open Source Software Package

AbstractMetaproteomics is an emerging research area which aims to reveal the functionality of microbial communities – unlike the increasingly popular metagenomics providing insights only on the functional potential. So far, the common approach in metaproteomics has been data-dependent acquisition mass spectrometry (DDA). However, DDA is known to have limited reproducibility and dynamic range with samples of complex microbial composition. To overcome these limitations, we introduce here a novel approach utilizing data-independent acquisition (DIA) mass spectrometry, which has not been applied in metaproteomics of complex samples before. For robust analysis of the data, we introduce an open-source software package diatools, which is freely available at Docker Hub and runs on various operating systems. Our highly reproducible results on laboratory-assembled microbial mixtures and human fecal samples support the utility of our approach for functional characterization of complex microbiota. Hence, the approach is expected to dramatically improve our understanding on the role of microbiota in health and disease.

scholarly journals Metaproteomics boosted up by untargeted data-independent acquisition data analysis framework

2020 ◽  
Author(s):  
Sami Pietilä ◽  
Tomi Suomi ◽  
Laura L. Elo
Keyword(s):  
Mass Spectrometry ◽  
Open Source Software ◽  
Previous Method ◽  
Mass Spectrometry Data ◽  
Analysis Framework ◽  
Spectral Library ◽  
Microbial Composition ◽  
Data Independent Acquisition ◽  
Open Source Software Package ◽  
First Time

AbstractMass spectrometry based metaproteomics is a relatively new field of research that provides the ability to characterize the functionality of microbiota. Recently, we were the first to demonstrate the applicability of data-independent acquisition (DIA) mass spectrometry to the analysis of complex metaproteomic samples. This allowed us to circumvent many of the drawbacks of the conventionally used data-dependent acquisition (DDA) mass spectrometry, mainly the limited reproducibility when analyzing samples with complex microbial composition. However, the previous method still required additional DDA data on the samples to assist the DIA analysis. Here, we introduce, for the first time, a DIA metaproteomics approach that does not require any DDA data, but instead replaces a spectral library generated from DDA data with a pseudospectral library generated directly from the metaproteomics DIA samples. We demonstrate that using the new DIA-only approach, we can achieve higher peptide yields than with the DDA-assisted approach, while the amount of required mass spectrometry data is reduced to a single DIA run per sample. The new DIA-only metaproteomics approach is implemented as open-source software package DIAtools 2.0, which is freely available from DockerHub.

scholarly journals Proteomic characterization of the normal human medial meniscus body using data‐independent acquisition mass spectrometry

2020 ◽  
Vol 38 (8) ◽  
pp. 1735-1745 ◽  
Author(s):  
Elin Folkesson ◽  
Aleksandra Turkiewicz ◽  
Martin Rydén ◽  
Harini Velocity Hughes ◽  
Neserin Ali ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Medial Meniscus ◽  
Data Independent Acquisition ◽  
Normal Human ◽  
Using Data

scholarly journals TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation

Entropy ◽  
2020 ◽  
Vol 22 (9) ◽  
pp. 1030
Author(s):  
Kevin Schneider ◽  
Benedikt Venn ◽  
Timo Mühlhaus
Keyword(s):  
Free Energy ◽  
Functional Characterization ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Enrichment Score ◽  
Energy Investment ◽  
Biological Responses ◽  
Novel Approach ◽  
Biological Studies

The objective of gene set enrichment analysis (GSEA) in modern biological studies is to identify functional profiles in huge sets of biomolecules generated by high-throughput measurements of genes, transcripts, metabolites, and proteins. GSEA is based on a two-stage process using classical statistical analysis to score the input data and subsequent testing for overrepresentation of the enrichment score within a given functional coherent set. However, enrichment scores computed by different methods are merely statistically motivated and often elusive to direct biological interpretation. Here, we propose a novel approach, called Thermodynamically Motivated Enrichment Analysis (TMEA), to account for the energy investment in biological relevant processes. Therefore, TMEA is based on surprisal analysis, which offers a thermodynamic-free energy-based representation of the biological steady state and of the biological change. The contribution of each biomolecule underlying the changes in free energy is used in a Monte Carlo resampling procedure resulting in a functional characterization directly coupled to the thermodynamic characterization of biological responses to system perturbations. To illustrate the utility of our method on real experimental data, we benchmark our approach on plant acclimation to high light and compare the performance of TMEA with the most frequently used method for GSEA.

Characterization of lipids in complex samples using comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry

2005 ◽  
Vol 1086 (1-2) ◽  
pp. 2-11 ◽  
Author(s):  
Eric Jover ◽  
Mohamed Adahchour ◽  
Josep M. Bayona ◽  
René J.J. Vreuls ◽  
Udo A.Th. Brinkman
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Time Of Flight ◽  
Two Dimensional ◽  
Complex Samples ◽  
Flight Mass Spectrometry

Hetero-Epitaxial Single Crystal 3C-SiC Opto-Mechanical Pressure Sensor

2015 ◽  
Vol 821-823 ◽  
pp. 902-905 ◽  
Author(s):  
Alberto Roncaglia ◽  
Ruggero Anzalone ◽  
Luca Belsito ◽  
Fulvio Mancarella ◽  
Massimo Camarda ◽  
...  
Keyword(s):  
Single Crystal ◽  
Pressure Sensor ◽  
Dynamic Range ◽  
Functional Characterization ◽  
Mechanical Pressure ◽  
Work Related ◽  
Pressure Application ◽  
Early Testing ◽  
Property Assessment

The design, fabrication, early testing and material property assessment work related to the development of an opto-mechanical pressure sensor implemented with hetero-epitaxial 3C-SiC on silicon is described. The sensor is constituted by a single-crystal 3C-SiC membrane whose deflection upon pressure application is measured using a fiber-optic interferometric readout. The fabrication of sensor prototypes and micromachined 3C-SiC membranes for test purposes is described and the results of bulge tests on the membranes are reported. Functional characterization of the sensor prototypes in the pressure range 0-3 bar is also presented, showing good linearity and reproducibility of the sensor response, sensitivity of roughly 2 mV/bar and estimated pressure resolution around 0.5 bar on a 0-200 bar dynamic range.

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