Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry

2018 ◽  
Vol 17 (10) ◽  
pp. 3418-3430 ◽  
Author(s):  
Katalin Barkovits ◽  
Andreas Linden ◽  
Sara Galozzi ◽  
Lukas Schilde ◽  
Sandra Pacharra ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cerebrospinal Fluid ◽  
Data Independent Acquisition

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

Characterization of cerebrospinal fluid by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry

2013 ◽  
Vol 1293 ◽  
pp. 142-149 ◽  
Author(s):  
Minna Hartonen ◽  
Ismo Mattila ◽  
Anna-Liisa Ruskeepää ◽  
Matej Orešič ◽  
Tuulia Hyötyläinen
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Cerebrospinal Fluid ◽  
Time Of Flight ◽  
Two Dimensional ◽  
Flight Mass Spectrometry

Characterization of Amyloid β Peptides in Cerebrospinal Fluid by an Automated Immunoprecipitation Procedure Followed by Mass Spectrometry

2007 ◽  
Vol 6 (11) ◽  
pp. 4433-4439 ◽  
Author(s):  
Erik Portelius ◽  
Ai Jun Tran ◽  
Ulf Andreasson ◽  
Rita Persson ◽  
Gunnar Brinkmalm ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cerebrospinal Fluid ◽  
Amyloid Β

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 Quantification of nuclear protein dynamics reveals chromatin remodeling during acute protein degradation

2018 ◽  
Author(s):  
Alexander J. Federation ◽  
Vivek Nandakumar ◽  
Hao Wang ◽  
Brian C. Searle ◽  
Lindsay K. Pino ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Dynamics ◽  
Nuclear Protein ◽  
Data Independent Acquisition ◽  
Transcriptional Dynamics ◽  
Associated Proteins ◽  
Bromodomain Proteins ◽  
Nuclear Proteome ◽  
Comprehensive Characterization

AbstractSequencing-based technologies cannot measure post-transcriptional dynamics of the nuclear proteome, but unbiased mass-spectrometry measurements of chromatin-associated proteins remain difficult. In this work, we have combined facile nuclear sub-fractionation approaches with data-independent acquisition mass spectrometry to improve detection and quantification of nuclear proteins in human cells and tissues. Nuclei are isolated and subjected to a series of extraction conditions that enrich for nucleoplasm, euchromatin, heterochromatin and nuclear-membrane associated proteins. Using this approach, we can measure peptides from over 70% of the expressed nuclear proteome. As we are physically separating chromatin compartments prior to analysis, proteins can be assigned into functional chromatin environments to illuminate systems-wide nuclear protein dynamics. The integrity of nuclear sub-compartments were validated with immunofluorescence, which confirms the presence of key markers during chromatin extraction. We then apply this method to study the nuclear proteome-wide response to pharmacological degradation of the BET bromodomain proteins. BET degradation leads to widespread changes in chromatin composition, and we discover global HDAC1/2-mediated remodeling of chromatin previously bound by BET bromodomains. In summary, we have developed a technology for reproducible, comprehensive characterization of the nuclear proteome to observe the systems-wide nuclear protein dynamics.

scholarly journals Extending the Proteomic Characterization of Candida albicans Exposed to Stress and Apoptotic Inducers through Data-Independent Acquisition Mass Spectrometry

mSystems ◽  
2021 ◽  
Author(s):  
Ahinara Amador-García ◽  
Inés Zapico ◽  
Ana Borrajo ◽  
Johan Malmström ◽  
Lucía Monteoliva ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Candida Albicans ◽  
Invasive Candidiasis ◽  
Health Problem ◽  
Fungal Infections ◽  
Immunocompromised Patients ◽  
Content Type ◽  
Data Independent Acquisition ◽  
Chronic Disorders

Fungal infections are a worldwide health problem, especially in immunocompromised patients and patients with chronic disorders. Invasive candidiasis, caused mainly by C. albicans , is among the most common fungal diseases.

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