TY  - JOUR
A1  - Kraus, Sara Milena
A1  - Mathew-Stephen, Mariet
A1  - Schapranow, Matthieu-Patrick
T1  - Eatomics
BT  - Shiny exploration of quantitative proteomics data
JF  - Journal of proteome research
N2  - Quantitative proteomics data are becoming increasingly more available, and as a consequence are being analyzed and interpreted by a larger group of users. However, many of these users have less programming experience. Furthermore, experimental designs and setups are getting more complicated, especially when tissue biopsies are analyzed. Luckily, the proteomics community has already established some best practices on how to conduct quality control, differential abundance analysis and enrichment analysis. However, an easy-to-use application that wraps together all steps for the exploration and flexible analysis of quantitative proteomics data is not yet available. For Eatomics, we utilize the R Shiny framework to implement carefully chosen parts of established analysis workflows to (i) make them accessible in a user-friendly way, (ii) add a multitude of interactive exploration possibilities, and (iii) develop a unique experimental design setup module, which interactively translates a given research hypothesis into a differential abundance and enrichment analysis formula. In this, we aim to fulfill the needs of a growing group of inexperienced quantitative proteomics data analysts. Eatomics may be tested with demo data directly online via https://we.analyzegenomes.com/now/eatomics/or with the user's own data by installation from the Github repository at https://github.com/Millchmaedchen/Eatomics.
KW  - R Shiny
KW  - application
KW  - label-free
KW  - proteomics
KW  - analysis
KW  - differential
KW  - abundance
KW  - experimental design
Y1  - 2021
U6  - https://doi.org/10.1021/acs.jproteome.0c00398
SN  - 1535-3893
SN  - 1535-3907
VL  - 20
IS  - 1
SP  - 1070
EP  - 1078
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Nordmeyer, Sarah
A1  - Kraus, Milena
A1  - Ziehm, Matthias
A1  - Kirchner, Marieluise
A1  - Schafstedde, Marie
A1  - Kelm, Marcus
A1  - Niquet, Sylvia
A1  - Stephen, Mariet Mathew
A1  - Baczko, Istvan
A1  - Knosalla, Christoph
A1  - Schapranow, Matthieu-Patrick
A1  - Dittmar, Gunnar
A1  - Gotthardt, Michael
A1  - Falcke, Martin
A1  - Regitz-Zagrosek, Vera
A1  - Kuehne, Titus
A1  - Mertins, Philipp
T1  - Disease- and sex-specific differences in patients with heart valve disease
BT  - a proteome study
JF  - Life Science Alliance
N2  - Pressure overload in patients with aortic valve stenosis and volume overload in mitral valve regurgitation trigger specific forms of cardiac remodeling; however, little is known about similarities and differences in myocardial proteome regulation. We performed proteome profiling of 75 human left ventricular myocardial biopsies (aortic stenosis = 41, mitral regurgitation = 17, and controls = 17) using high-resolution tandem mass spectrometry next to clinical and hemodynamic parameter acquisition. In patients of both disease groups, proteins related to ECM and cytoskeleton were more abundant, whereas those related to energy metabolism and proteostasis were less abundant compared with controls. In addition, disease group-specific and sex-specific differences have been observed. Male patients with aortic stenosis showed more proteins related to fibrosis and less to energy metabolism, whereas female patients showed strong reduction in proteostasis-related proteins. Clinical imaging was in line with proteomic findings, showing elevation of fibrosis in both patient groups and sex differences. Disease-and sex-specific proteomic profiles provide insight into cardiac remodeling in patients with heart valve disease and might help improve the understanding of molecular mechanisms and the development of individualized treatment strategies.
Y1  - 2023
U6  - https://doi.org/10.26508/lsa.202201411
SN  - 2575-1077
VL  - 6
IS  - 3
PB  - EMBO Press
CY  - Heidelberg
ER  -