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 Proteomic comparison of osteoarthritic and reference human menisci using data-independent acquisition mass spectrometry

2020 ◽  
Vol 28 (8) ◽  
pp. 1092-1101
Author(s):  
E. Folkesson ◽  
A. Turkiewicz ◽  
N. Ali ◽  
M. Rydén ◽  
H.V. Hughes ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Independent Acquisition ◽  
Using Data

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 Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry

2016 ◽  
Vol 12 (8) ◽  
pp. 2385-2388 ◽  
Author(s):  
Simone Sidoli ◽  
Rina Fujiwara ◽  
Katarzyna Kulej ◽  
Benjamin A. Garcia
Keyword(s):  
Mass Spectrometry ◽  
Data Independent Acquisition ◽  
Modified Peptides ◽  
Using Data

Data-independent acquisition (DIA) is here applied to determine unexplored phosphorylation events on isobarically modified peptides.

scholarly journals Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry

2015 ◽  
Vol 14 (8) ◽  
pp. 3252-3262 ◽  
Author(s):  
Kimberly A. Krautkramer ◽  
Lukas Reiter ◽  
John M. Denu ◽  
James A. Dowell
Keyword(s):  
Mass Spectrometry ◽  
Histone Modifications ◽  
Data Independent Acquisition ◽  
Using Data

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

2015 ◽  
Vol 8 (380) ◽  
pp. rs6-rs6 ◽  
Author(s):  
Benjamin L. Parker ◽  
Guang Yang ◽  
Sean J. Humphrey ◽  
Rima Chaudhuri ◽  
Xiuquan Ma ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Insulin Signaling ◽  
Data Independent Acquisition ◽  
Using Data
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