Research Groups

Mass Spectrometry at Dresdner Campus: A Road Map

MS Community Dresden:

The MS Community provides support to biological and clinical research projects carried at the Campus. It comprises MS-Facilities and MS-research groups from the MPI CBG, UKD, CMCB (TUD) and NCT, and Lipotype GmbH. The sites host more than 20 high-end MS instruments and have expertise in MS-based Lipidomics, Proteomics and Metabolomics. We work on service base and open for research collaborations. To our activities belong regular meetings, organization of ms-events, MS journal club and scientific consulting.

2021

Omics Flash Talks

Our annual get-together in the format of flash talks. Please join our friendly talks, share the news on your omics scientific landscape and stay connected.

Host: Andrej Shevchenko

Date and time: 26.01.2020, 14:00-17:00.

Location: ZOOM https://zoom.us/j/5587099875

 

14:00-14:05

Dr. Andrej Shevchenko

Welcome and introduction

 

14:05-14:15

Dr. Ignacy Rzagalinski

Fast-tracking QconCAT approach for absolute protein quantification

Shevchenko lab, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

14:15-14:25

Dr. Bharath Raghuraman

Absolute quantification: Pathway to proteome

14:25-14:35

Dr. Christian Klose

Lipotype's Highlights in 2020

Lipotype, Dresden, Germany

14:35-14:45

Nikolai Köhler, PhD researcher

Systemic Lipidome Alterations in HCC-induced Cachexia

Pauling lab, Computational Systems Medicine on Lipids and Metabolism,  Technical University Munich, Germany

14:45-14:55

BREAK  for coffee and chat

14:55-15:05

Tim Rose, PhD researcher &

Dr. Olga Vvedenskaya

Spartans project: subgroups of NAFL patients based on lipidomics

Pauling lab & Shevchenko lab

15:05-15:15

Anna TkachevPhD researcher

Extensive feature degenerecies in untargeted LC-MS experiments: how many lipid compounds are we quantifying?

Khaitovich lab, Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia

15:15-15:25

Aleskandra MitinaPhD researcher

Role of breast milk lipid composition in postnatal brain development

15:25 - 15:35

Dr. Matthias Pietzke

Towards a More Reliable Identification of Isomeric Metabolites Using Pattern Guided Retention Validation

Kempa lab, Proteomics and Metabolomics Platform, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany

15:35-15:50

Dr. Christof Mitterer

Nano-pillar columns separation technique from Microfluidics

PharmaFluidics NV, Gent, Belgium

15:50-16:00

BREAK  for coffee and chat

16:00-16:10

Dr. Marcus Höring

Updates from Liebisch lab and future plans

Liebisch lab, Clinical Chemistry and Laboratory Medicine, University of Regensburg, Germany

16:10-16:20

Dr. Iqbal Mahmud

Unraveling Fusobacterium nucleatum Mediated Metabolic Pathway Alterations in Cancer Cells  using High Resolution Mass Spectrometry

Garrett Laboratory, Department of Pathology, Immunology, and Laboratory medicine, College of Medicine |University of Florida, FL, USA

16:20-16:30

Dr. Sofia Traikov

Metabolomics in Dresden Campus and future plans

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

16:30-16:40

Dr. Pia Hoenscheid

The national Covid project and future plans

National Center for Tumor Diseases, Dresden, Germany

16:40-16:45

Dr. Andrej Shevchenko

Closing remarks

 

 

Journal club

Host: Bharath

Topic: Quantitative shotgun proteome analysis by direct infusion

Paper: https://www.nature.com/articles/s41592-020-00999-z

Date and time: 19.01.2021, 14:00.

Location: ZOOM https://zoom.us/j/5587099875

 

 

 

 

 

 

 

 

 

2020

Journal club

Host: Alessandra

Topic: Fatty Acid Methyl Ester Profiles of Bat Wing Surface Lipids​

Paper: link.springer.com/article/10.1007/s11745-014-3951-2

Date and time: 15.12.2020, 14:00.

Location: ZOOM https://zoom.us/j/5587099875

 

MS4U Journal club

Host: Barbara Borgonovo (PEPC group) and MS Community

Topic: Direct characterization of overproduced proteins by native mass spectrometry

Paper: https://www.nature.com/articles/s41596-019-0233-8

Date and time: 01.12.2020, 14:00.

Location: ZOOM https://zoom.us/j/5587099875

 

Journal club

Host: Yuting

Topic: Machine learning reveals serum sphingolipids as cholesterol-independent biomarkers of coronary artery disease

Paper: https://dm5migu4zj3pb.cloudfront.net/manuscripts/131000/131838/cache/131838.3-20200219144527-covered-253bed37ca4c1ab43d105aefdf7b5536.pdf

Date and time: 17.11.2020, 14:00.

Location: ZOOM https://zoom.us/j/5587099875

 

 

MS4U Journal club

Host: Vinca (Tomancak and Rodenfels groups) and Tobi (Shevchenko lab)

Topic: Remodeling of the metabolome during early frog development

Paper: https://doi.org/10.1371/journal.pone.0016881

Date and time: 03.11.2020, 14:00.

Location: ZOOM https://zoom.us/j/5587099875

 

Journal club

Host: Olya

Topic: Discovering a critical transition state from nonalcoholic hepatosteatosis to nonalcoholic steatohepatitis by lipidomics and dynamical network biomarkers

Paper: https://academic.oup.com/jmcb/article/8/3/195/2588620

Date and time: 15.09.2020, 14:00.

Location: Seminar Room 1, MPI-CBG

Journal club

Host: Kai

Topic: The single-cell pathology landscape of breast cancer

Paper: https://www.nature.com/articles/s41586-019-1876-x (and basic principle here for the A-graders https://www.nature.com/articles/nmeth.2869)

Date and time: 01.09.2020, 14:00.

Location: Seminar Room 1, MPI-CBG and ZOOM https://zoom.us/j/5587099875

Journal club

Host: Bharath
Topic: Rapid, deep and precise profiling of the plasma proteome with multinanoparticle protein corona
Paper: https://www.nature.com/articles/s41467-020-17033-7
Date and time: 11.08.2020, 14:00.
Location: Seminar Room 1, MPI-CBG and ZOOM https://zoom.us/j/5587099875

Journal club

Host: Jacobo
Topic: IsoSpec2: Ultrafast Fine Structure Calculator
Paper: https://pubs.acs.org/doi/10.1021/acs.analchem.0c00959
Date and time: 28.07.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Excel@Python course, session 3

Host: Jacobo
Topic: How to replace Excel with Python and automate everything?
Date and time: 24.07.2020, 14:00-16:00.
Location: MPI-CBG, Seminar Room 2 and/or Zoom https://us02web.zoom.us/j/5587099875

Excel@Python course, session 2

Host: Jacobo
Topic: How to replace Excel with Python and automate everything?
Date and time: 17.07.2020, 14:00.
Location: MPI-CBG, Seminar Room 1

Journal club

Host: Cedric
Topic: The proteome landscape of the kingdoms of life
Paper: https://www.nature.com/articles/s41586-020-2402-x.pdf
Date and time: 14.07.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Excel@Python course, session 1

Host: Jacobo
Topic: How to replace Excel with Python and automate everything?
Date and time: 10.07.2020, 14:00.
Location: MPI-CBG, Seminar Room 2

Journal club

Host: Tobias
Topic: DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
Paper by link https://www.nature.com/articles/s41592-019-0638-x AND https://github.com/vdemichev/diann
Date and time: 30.06.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Ignacy
Topic: Robust, reproducible and quantitative analysis ofthousands of proteomes by micro-flow LC–MS/MS
Paper by link https://www.nature.com/articles/s41467-019-13973-x#Sec19
Date and time: 16.06.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Oskar
Topics: Validation of lipidomic analysis of human plasma and serum by supercritical fluid chromatography–mass spectrometry and hydrophilic interaction liquid chromatography–mass spectrometry AND
Evaluation of lipid quantification accuracy using HILIC and RPLC MSon the example of NIST® SRM® 1950 metabolites in human plasma
Date and time: 09.06.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Kai
Topic: Structural Elucidation of Ether Glycerophospholipids Using Gas-Phase Ion/Ion Charge Inversion Chemistry
Date and time: 02.06.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

https://zoom.us/j/5587099875Journal club

Host: Canan
Topic: STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse
Paper: https://www.nature.com/articles/s41597-019-0202-7
Date and time: 26.05.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Olya & Bharath
Topic: Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics
Date and time: 19.05.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Alessandra Palladini
Topic: Characterization of the Lipidomic Profile of Human Coronavirus-Infected Cells: Implications for Lipid Metabolism Remodeling upon Coronavirus Replication
Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357182/
Date and time: 12.05.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Andrej Shevchenko
Topic: Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue
Paper: File attached
Date and time: 05.05.2020, 13:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Olga Vvedenskaya
Topic: Newborn Screening by Tandem Mass Spectrometry. Ethical and Social Issues
Paper: File attached
Video: Introduction to Bioethics: Bioethics & the Human Body.
Date and time: 28.04.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

The next JC paper is going to be informatic-y. Please join our discussion!

Host: Jacobo Miranda Ackerman
Topic: Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees
Paper: File attached
Date and time: 21.04.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Canan Has
Topic: Detecting fabrication in large-scale molecular omics data
Paper: File attached
Date and time: 07.04.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875

Journal club

Host: Olya Vvedenskaya
Topic: Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts.
Date and time: 31.03.2020, 14:00
Location: ZOOM https://zoom.us/j/5587099875
Paper: https://www.nature.com/articles/s41467-019-14044-x.pdf
You are welcome to join. Please read the JC rules below.

We are going to have coffee breaks in Zoom once in a while just for a chat.
If you would like to join the coffee break please drop an email to olga.vvedenskayampi-cbg.de.

Journal club

Host: Olya Vvedenskaya
Date and time: 28.01.2020, 14:00 – 15:00
Location: MPI-CBG, Seminar room 1
Paper: High Expression of Glycolytic Genes in Cirrhosis Correlates With the Risk of Developing Liver Cancer
https://www.frontiersin.org/articles/10.3389/fcell.2018.00138/full
You are welcome to join. Please read the JC rules below.

Journal club

Host: Canan Has
Date and time: 14.01.2020, 14:00 – 15:00
Location: MPI-CBG, Seminar room 1
Paper: Longitudinal multi-omics of host–microbe dynamics in prediabetes
https://www.nature.com/articles/s41586-019-1236-x.pdf
You are welcome to join. Please read the JC rules.

The JC rules are the following:

  1. The assigned person choses the paper in advance and sends it around, but does not present it.
  2. Most importantly, Everyone Reads the Paper!
  3. Starting person (randomly chosen) describes (questiones, criticizes) the first figure/paragraph/topic, and all together we try to figure out what authors wanted to say. The second person (randomly chosen) describes the second figure and so on.
  4. Please come if you read the paper.
  5. If you bring your colleagues or friends, make sure that they are aware of the rules.