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), CRTD 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.
MS Community Journal Club
Moderator: Marc Gentzel
Topic: Summer Digest
Paper: present interesting article of your choice published this summer, 2-3min.
Everybody welcome!
Please, drop your paper titles to Marc (marc.gentzel@tu-dresden.de) before the session.
Date: September 15th 2023, 2pm CEST
Zoom: tba
MS Community Journal Club
Speaker: Pia Hoenscheid, MALDI Imaging Unit NCT, Dresden
Topic: MS imaging
Paper: https://www.nature.com/articles/s41467-023-38403-x
Date and place: Jul 4th 2023, 2pm CEST, Zoom
https://eu02web.zoom.us/j/69460141900?pwd=MzIwYUNDMzVlcS9iUFJGUnZ6K2t5UT09
Meeting ID: 694 6014 1900
Passcode: 758571
MS Community Journal Club
Speaker: Simon Devos, VIB Ghent, Belgium
Topic: Beyond Massspec - New Generation Proteomics
Date: June 13th, Tue, 2pm CEST
Location:https://eu01web.zoom.us/j/67206726496?pwd=UGhjaWJSV3JDdm1COHVZRDRKSXRkdz09
Meeting ID: 672 0672 6496
Passcode: 433669
MS Community Journal Club
Speaker: Olya Vvedenskaya
Topic: Metabolomic profiles predict individual multidisease outcomes
Paper: https://www.nature.com/articles/s41591-022-01980-3
Date: June 6th, Tue, 2pm CEST
Location: https://eu01web.zoom.us/j/66739474186?pwd=WTR0eG41WGNZbmNYTnRpQ3l5cGJaQT09
Meeting ID: 667 3947 4186
Passcode: 670574
Everybody welcome!
Extraordinary MS Community session
Host: Marc Gentzel, TUD
Guests: Verena Tellström (Bruker Daltonics GmbH) and Richard Broadhead (Seer Inc)
Titles: Novel Tools in Proteomics and Clinical Biomarker Discovery
Date: May 3rd, 3pm, in-person
Location: Dresden Campus, Tatzberg 41, B Cube, Seminar Room E73/74
Everybody welcome!
MS Community Journal Club
Host: Marc Gentzel, CMCB TU Dresden
Speaker: Dr. Jan Bucek, Plasmion GmbH
Topic: SICRIT ionization source - New Dimensions in Mass Spectrometry
Soft Ionization by Chemical Reaction in Transfer (SICRITis) a new plug-and-play ionization source for quantitative analyses on any-vendor LCMS systems. https://www.plasmion.de/products
Date: 18.04.2023 14:00 CET
Location: https://eu01web.zoom.us/j/62431670888?pwd=VHpmNDJCM2hkeWFBbmgxSkUxTEV0Zz09
Meeting ID: 624 3167 0888
Passcode: 129466
MS4U Journal Club Session
Everybody is welcome!
Speakers: Christian Klose (Lipotype) and Andrej Shevchenko (MPI CBG)
Topic: How gender impacts the lipidome?
Papers: https://pubmed.ncbi.nlm.nih.gov/36193934/, https://www.nature.com/articles/srep27710
Date: 28.03.2023, 14:00 CET
https://eu01web.zoom.us/j/69310145483?pwd=RWw3cUtrUUVZTUNaVVArQytISytaZz09
Meeting ID: 693 1014 5483
Passcode: 395398
Journal club
Speaker: Jonas Poehls (CSBD/CBG)
Topic: About weird and novel proteins
Paper: https://doi.org/10.1016/j.mcpro.2022.100480
Date: 21.03.2023, 14:00 CET
Location: MPI-CBG, Seminar Room 3
MS Community Journal Club
Host: Fedorova Lab, Center of Membrane Biochemistry and Lipid Research, TUD
Speaker: Zhixu Ni
Topic: Explore the dark forest of LipidA
Paper: https://doi.org/10.1021/acs.analchem.1c03566
Date: 14.03.2023 14:00 CET
https://eu01web.zoom.us/j/65172829327?pwd=NDRvL2FLSEFuVkJNKy9XNk9lMTVjdz09
Meeting ID: 651 7282 9327
Passcode: 683960
MS Community Journal Club
Host: Andrej Shevchenko
Speaker: Dr. Eduard Sabido, CRG Barcelona
Topic: Cloud based Quality Control System for Mass Spectrometry Laboratories
Paper: https://doi.org/10.1021/acs.jproteome.0c00853 and https://doi.org/10.1371/journal.pone.0189209
Date: 22.02.2023, 14:00 CET
Location: Zoom, https://eu01web.zoom.us/j/69536557484?pwd=SE1paGNaU3ArbUt3R2tpZTI0eVoyUT09
Meeting ID: 695 3655 7484
Passcode: 773823
Journal Club
Host: Vannur Garikapati
Topic: New Super-Resolution Mass Spec for Proteomics
Paper: https://pubs.acs.org/doi/10.1021/acs.analchem.2c04742
Date: 14.02.2023, 14:00 CET in-person
Location: MPI-CBG, Gallery
MS Community Journal Club
Host: Andrej Shevchenko
Speaker: Dale Cooper-Shepherd, Waters Inc.
Topic: Novel Hybrid Quadrupole-Multireflecting Time-of-Flight Mass Spectrometry System
https://doi.org/10.1021/jasms.2c00281
Date: 07.02.2023, 14:00 CET
Location: https://us02web.zoom.us/j/86267848379?pwd=LytnVTFSWWJvcGh0MnRnVUNxaFoyUT09
Meeting ID: 862 6784 8379
Passcode: 637141
Extraordinary MS Community session
Guest: Dr. Stephan Beil, CFEA coordinator, Faculty of Environmental Sciences TUD
Topic: Presentation of the new Core Facility Environmental Analytics (CFEA) at TUD
Date: Monday, 30.01.2023, 14:00 CET Zoom
Location: https://us02web.zoom.us/j/83508933360?pwd=MlA4Tk1KL1B6dk9Gemx6Y1V3eUR3QT09
Meeting ID: 835 0893 3360
Passcode: 976021
Journal Club
Host: Silvia Radrezza
Topic: pubs.acs.org/doi/abs/10.1021/acs.analchem.2c02042
Date: 24.01.2023 14:00 CET in-person
Location: MPI-CBG, Seminar Room 1
Journal Club
Host: Andrej Shevchenko
Topic: https://doi.org/10.1101/2022.08.26.505407
Date: 17.01.2023 14:00 CET in-person
Location: MPI-CBG, Seminar room #3
This year we will host our FIFTH anniversary traditional get-together! X-Mass updates is an event that is open to all.
Host: Andrej Shevchenko
Date and time: 06.12.2022, 14:00-17:00 CET
Short overview: youtu.be/2bTtMl9BaO4
| Time | Speaker | Affiliation | Titles |
| 14:00-14:05 | Andrej Shevchenko | Shevchenko Lab, MPI-CBG, Dresden | Welcome |
| 14:05-14:15 | Silvia Radrezza | Shevchenko Lab, MPI-CBG, Dresden | Laser capture microdissection for spatial resolved lipidomics and proteomics |
| 14:15-14:25 | Christer Ejsing | Ejsing Lab, SDU, Denmark | An oral choline tolerance test with systems-level metabolic flux profiling |
| 14:25-14:35 | Zhixu Ni | Fedorova Lab, ZMBL, TUD, Dresden | Build your data analysis pipeline for lipidomcis |
| 14:35-14:45 | Robert Ahrends | Ahrends Lab, University of Vienna, Austria | Strategies for the exploration of large-scale lipidomics studies |
| 14:45-14:55 | Christian Klose | Lipotype, Dresden | Lipotype R&D updates 2022 |
| 14:55-15:10 | Break | breakout room for speakers session 1 | |
| 15:10-15:20 | Bernhard Küster | Küster Lab, TUM, Germany | Proteome expression profiling in response to drugs by single-shot micro-LC-FAIMS-MS/MS |
| 15:20-15:30 | Alex von Appen | von Appen Lab, MPI-CBG, Dresden | Discovery-driven Structural Biology with Proteomics and AlphaFold |
| 15:30-15:40 | Ignacy Rzagalinski | Shevchenko Lab, MPI-CBG, Dresden | Absolute quantification of neurological protein markers by FastCAT workflow |
| 15:40-15:50 | Josch Pauling | Pauling Lab, TUM, Germany | All I want for Christmas: Smart Tools for lipidomics data analyses |
| 15:50-16:00 | Jens Rister | Rister Lab, UMass Boston, US | A fly eye therapy for vitamin A deficiency |
| 16:00-16:15 | Break | breakout room for speakers session 2 | |
| 16:15-16:25 | Anna Shevchenko | Shevchenko Lab, MPI-CBG, Dresden | Let it glow: Absolute Quantifcation of Fluorescent Proteins |
| 16:25-16:35 | Vadim Arshavsky | Arshavski Lab, Duke University, US | Simultaneous absolute quantification of multiple proteins from the photoreceptor outer segment |
| 16:35-16:45 | Canan Has | Centogene, Germany | Advancing rare disease patient diagnostics and treatment with multiomics |
| 16:45-16:55 | Yury Tsybin | Spectroswiss, Switzerland | Suspect-driven direct feature extraction in metabolomics and proteomics |
| 16:55-17:00 | Andrej Shevchenko | Shevchenko Lab, MPI-CBG, Dresden | Closing remarks |
You can check the info about previous X-Mass updates below by selecting the year you are interested in.
Host: Mirko Peitzsch
Topic: Development of an Accurate Mass Retention Time Database for Untargeted Metabolomic Analysis and Its Application to Plasma and Urine Pediatric Samples
Paper: https://www.mdpi.com/1420-3049/26/14/4256/htm
Date and time: 22.11.2022, 14:00 CET.
Location: https://us02web.zoom.us/j/86402738879?pwd=bVh3U29ucmwrbmFXNUZ3b1NiVERqdz09
Host: Sofia Traikov
Topic: Analysis of endocannabinoids and cortisol in hairs
Speaker: Dr. Wei Gao (Biopsychology, TU Dresden)
Paper: doi: doi.org/10.1016/j.cca.2022.09.026 and doi.org/10.1016/j.pnpbp.2022.110658
Date and time: 15.11.2022, 14:00 CET.
Location: https://us02web.zoom.us/j/84144832724?pwd=bHRPaFFBeEY5UE5xTDBGRXpUZHNYUT09
Speaker: Mikael Simons
Topic: Role of lipids in CNS regeneration
Date and time: 25.10.2022 17:00 CEST
More info and Registration: https://www.lipotype.com/lipidomics-webinars/role-of-lipids-in-central-nervous-system-regeneration/
Host: Vannur Garikapati
Topic: "Quantitative profiling of octadecanoids (oxylipins) using SFC-MS/MS and LC-MS/MS"
Paper: https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c02601
Date and time: 18.10.2022, 14:00.
Location: Zoom https://us02web.zoom.us/j/83356276311?pwd=QnV0UHQxeHNGa2dBSFl0WkNnNVlyUT09
Meeting ID: 833 5627 6311
Passcode: 284374
Host: MS Dresden Community and Marc Gentzel
Topic: Summer Digest
Paper: Let us know if you read anything cool!
#ms fundamentals: 10.1002/ange.202202165
#proteomics: 10.1021/acs.analchem.2c02777
#lipidomics: 10.1038/s41598-022-14690-0
#bioinformatics: 10.1038/s41592-022-01496-1
10.1186/s13059-022-02625-x
#metabolomics: 10.1002/anie.201904416
Date and time: 14.09.2022 14:00 CEST
Location: ZOOM https://zoom.us/j/5587099875
Speaker: Ilya Levental
Topic: Composition, Organization & Function of Plasma Membranes
Date and time: 13.09.2022 17:00 CEST
More info and Registration: www.lipotype.com/lipidomics-webinars/composition-organization-and-function-of-plasma-membranes/
Host: Anna Shevchenko
Topic: Single-molecule protein sequencing
Paper: doi: 10.1063/5.0065509 and doi.org/10.1038/s41592-021-01143-1
Date and time: 12.07.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Speaker: Prof. Kai Simons
Topic: What Have Lipids to Do With the Worst Pandemic Ever?
Date and time: 29.06.2022 17:00
More info and Registration: www.lipotype.com/lipidomics-webinars/lipids-and-the-obesity-pandemic/
Host: Yuting Wang (former Shevchenko) and Maren Rudolph (Zeissig Group, TU Hospital/CRTD)
Topic: Clinical Lipidomics. Sortase A-cleavable CD1d identifies sphingomyelins as major class of CD1d-associated lipids.
Paper: https://www.frontiersin.org/articles/10.3389/fimmu.2022.897873/abstract
Date and time: 28.06.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Ignacy Rzagalinski
Topic: Global Extraction from Parallel Reaction Monitoring to Quantify Background Peptides for Improved Normalization and Quality Control in Targeted Proteomics
Paper: https://pubs.acs.org/doi/10.1021/acs.analchem.1c01375?ref=pdf
Date and time: 14.06.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Marc Gentzel (MS Facility, TU Dresren)
Speaker: Dr. Weißker/Dr.Roudini, Leibniz Institute for Solid State and Materials Research Dresden (IFW)
Topic: Nanotechnology and Aerosol Generation
Paper: https://pubs.rsc.org/en/content/articlelanding/2015/lc/c5lc00756a/unauth
Date and time: 18.05.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Speaker: Andrej Shevchenko
Topic: Direct analysis of tissue biopsies could be in a better position to elucidate pathophysiological mechanisms than liquid biopsies.
Date and time: 17.05.2022 17:00
More info and Registration: https://www.lipotype.com/lipidomics-webinars/shotgun-lipidomics-of-tissue-biopsies
Video: youtu.be/reVBBEKdDIM
Speaker: Christian Klose
Topic: Yeast is a powerful model system for cell and molecular biology research. What should be considered when conducting yeast lipidomics?
Date and time: 05.04.2022 17:00
More info and Registration: www.lipotype.com/how-to-yeast-lipidomics-research
Host: Maria Fedorova Lab
Topic: Achieving Absolute Molar Lipid Concentrations: A Phospholipidomics Cross-Validation Study
Paper: https://pubs.acs.org/doi/10.1021/acs.analchem.1c03743
Date and time: 22.03.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Silvia Radrezza
Topic: Handheld Mass Spectrometer with Intelligent Adaptability for On-Site and Point-of-Care Analysis
Paper: https://doi.org/10.1021/acs.analchem.1c02508
Date and time: 15.03.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Speaker: Mathias Gerl
Topic: The amount and complexity of lipidomics data sets can be intimidating initially - but this does not need to be the case.
Date and time: 24.02.2022 17:00
More info and Registration: www.lipotype.com/lipidomics-webinars/how-to-make-sense-of-lipidomics-data
Host: Jonas Pohls (Agnes Toth-Petroczy/Shevchenko labs) and MS Community
Topic: Interplay between transcriptomics and proteomics
Paper: https://doi.org/10.1016/j.molcel.2020.03.031
Date and time: 22.02.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Tobias Jumel
Topic: Does Data-Independent acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer's Disease
Paper: pubs.acs.org/doi/10.1021/acs.jproteome.1c00558
Date and time: 08.02.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Kai Schuhmann
Topic: Nontargeted High-Resolution Mass Spectrometric Workflow for the Detection of Butyrylcholinesterase-Derived Adducts with Organophosphorus Toxicants and Structural Characterization of Their Phosphyl Moity after In-Source Fragmentation
Paper: pubs.acs.org/doi/abs/10.1021/acs.analchem.1c04116
Date and time: 25.01.2022, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
August 2023
Maria Fedorova, Andrej Shevchenko, Kai Schuhmann, and James Saenz will give lectures at the upcoming ILS conference, and Olya Vvedenskaya will talk about scientific community building for the clinical lipidomics interest group. Five lipidomics talks from Dresden this year. See you in Vienna at the end of August!
Center of Membrane Biochemistry and Lipid Research
Core Facility Environmental Analytics
Experimental MS unit at University Clinic Carl Gustav Carus
Lipid metabolism Research group
Mass Cytometry Facility (CYTOF) Facility at the CRTD
MS4U was launched in 2020 to build a bridge between MS Community and scientists working in biological and clinical research at Dresdner campus. Here we discuss articles selected by YOU.
You found a hot paper related to your scientific topic but...
- do not understand ms-method?
- unsure if it fosters YOUR project?
- unclear if this is routine or only runs in a single lab?
- and, how it practically works?
Once you suggest an article or topic, we will look for complementary articles published by leading practitioners in this field and then analyze them together with you. MS-Lipidomics, MS-proteomics, MS-metabolomics, MS-imaging, any MS - let's discuss it with MS-Profis from the entire Dresden campus!
Submit YOUR HOT PAPER suggestion by clinical.lipidomics@mpi-cbg.de
2021 Events
Host: Andrej Shevchenko
Date and time: 07.12.2021 14:00-17:00
Location: https://zoom.us/j/99494697998?pwd=Q0xBZzBNdHdYSk1PRmdjMXltS2dkQT09 and MPI-CBG
14:00 -14:05 | Dr. Andrej Shevchenko | Welcome and Introduction | Host |
14:05 -14:15 | Dr. Ignacy Rzagalinski | Consistent and sensitive absolute quantification of proteins in liquid biopsies by FastCAT workflow | Shevchenko Lab |
14:15 - 14:25 | Dr. Sofia Traikov | Blood porphyrins are prognostic markers of developing COVID-19 | Metabolomics Unit, MPI CBG, Dresden |
14:25 - 14:35 | Dr. Christian Klose | Lipotype Shotgun Lipidomics - Highlights in 2021 | CTO, Lipotype GmbH, Dresden |
14:35- 14:45 | Dr. Yury Tsybin | On the Value of the Unreduced Data for Orbitrap-Driven Omics | Spectroswiss Sarl, Lausanne, Switzerland |
14:45 - 14:55 | Dr. Robert Ahrends | Multiomics of synaptic junctions reveals altered lipid metabolism and signaling following environmental enrichment | Ahrends Lab, Fakultät für Chemie, University of Vienna, Austria |
14:55 - 15:05 | break | chatroom will be open for discussion and questions |
|
15:05 - 15:15 | Dr. Kai Schuhmann | Molecular composition and dynamics of the lipidome by ultra-high resolution shotgun mass spectrometry | Shevchenko Lab |
15:15 - 15:25 | Dr. Andre Nadler | Analysing lipid metabolism and transport on sub-cellular scales | Nadler Lab, MPI CBG, Dresden |
15:25 - 15:35 | Dr. Dale Cooper-Shepherd | What's happening with Cyclic Ion Mobility-Mass Spectrometry? | Senior Scientist, Waters Inc., Wilmslow, UK |
15:35 -15:45 | Dr. Maria Fedorova | Digging into the epilipidome: dysregulation of lipid modifications in human obesity and type II diabetes | Fedorova Lab, Centre for Membrane Biochemistry and Lipid Research, TU Dresden |
15:45 -15:55 | Dr. Olga Vvedenskaya | Off bench experience: how to get there and what to expect? | Spectroswiss, Lausanne, Switzerland |
15:55- 16:05 | break | chatroom will be open for discussion and questions |
|
16:05 -16:15 | Dr. Bharath Kumar Raghuraman | New approaches in quantitative analysis of proteins | Evosep, Odense, Denmark |
16:15 - 16:25 | Dr. Eduardo Jacobo Miranda Ackerman | Engineering the New Generation of LipidXplorer | Shevchenko Lab |
16:25 - 16:35 | Dr. Pia Hoenscheid/Linna Sommer | MALDI Imaging in the pathology - gastric carcinoma as a new target for diagnostic stratification by mass spec patterns | MALDI Imaging Unit, National Centre for Tumor Diseases, Dresden |
16:35 - 16:45 | Tim Daniel Rose, PhD researcher | Revealing mechanisms of lipidomic dysregulation with the Lipid Network Explorer | Pauling Lab, LipiTUM, Experimental Bioinformatics, TU Munich, Germany |
16:45 -16:55 | Dr. Gerhard Liebisch, Dr. Marcus Höring | Highlights of Lipidomics Regensburg in 2021 | Liebisch Lab, Clinical Chemistry and Laboratory Medicine, University Regensburg, Germany |
16:55 -17:00 | Dr. Andrej Shevchenko | Closing remarks | Host |
Host: Andrej Shevchenko
Speaker: Dr. Wei Gao, a leader of MS unit at the Faculty of Psychology, TU Dresden
Topic: Research of stress biomarker based on LC-MS/MS
Date and time: 30.11.2021, 14:00.
Location: https://zoom.us/j/5587099875
Speaker: Christian Klose
Topic: Population health studies frequently rely on omics technologies but biomarker identification studies benefit only if the data are of high quality and reliably reproducible.
Date and time: 02.12.2021 17:00
More info and Registration: www.lipotype.com/lipidomics-webinars/why-population-health-studies-must-run-lipidomics
Host: Andrej Shevchenko
Speaker: Maria Fedorova, a group leader at the Center of Membrane Biochemistry and Lipid Research at the Medical Faculty of the TU Dresden
Topic: Lipid metabolism: analysis and integration
Date and time: 16.11.2021, 14:00.
Location: https://zoom.us/j/5587099875
Speaker: Christian Klose
Topic: Mouse has shown a remarkable specificity of lipids in different cells, tissues, and organs. The mouse lipidomics atlas facilitates experimental design and interpretation in mouse studies.
Date and time: 19.10.2021 17:00
More info and Registration: www.lipotype.com/lipidomics-webinars/mouse-lipidomics-for-clinical-research/
Host: Canan Has
Topic: New open-source tools for MS-based proteomics
Paper: https://www.nature.com/articles/s41467-021-22303-zhttps://doi.org/10.1093/bioinformatics/btab674
https://doi.org/10.1101/2021.07.23.453379https://www.nature.com/articles/s41467-021-22303-z
www.nature.com/articles/s41467-021-22303-z
Date and time: 12.10.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
3 talks 3 minutes each:
1. Dr. Marc: NHS-Ester Tandem Labeling in One Pot Enables 48-Plex Quantitative Proteomics
2. Dr. Kai: Isomer Selective Comprehensive Lipidomics Analysis of Phosphoinositides in Biological Samples by Liquid Chromatography with Data Independent Acquisition Tandem Mass Spectrometry
3. pre-Dr. Tobi: Ultra-fast proteomics with Scanning SWATH
4. Q&A and general discussion
Date and time: 28.09.2021 14:00
Location: ZOOM https://zoom.us/j/5587099875
Speaker: Kai Simons
Topic: Lipid metabolism homeostasis is essential for life, but the ongoing obesity pandemic threatens it. Blood lipidomics profiles may help stem the obesity affliction. Lipids are coming back.
Date and time: 21.09.2021 17:00
More info and Registration: https://www.lipotype.com/lipidomics-webinars/introduction-to-lipids-and-lipidomics/
Host: Andrej Shevchenko
Speaker: Claudia Peitzsch
Topic: Introduction to the suspension mass cytometry method
Paper: https://www.nature.com/articles/s41467-021-22303-z
Date and time: 08.06.2020, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Agenda:
1. Olya will talk about Lipidomics and Organoids ~15 mins
2. Sofia will talk about Metabolomics and Organoids ~15 mins
3. Ignacy will talk about Proteomics and Organoids ~15 mins
4. Q&A and general discussion
Date and time: 01.06.2021 14:00
Location: ZOOM https://zoom.us/j/5587099875
Host: Kai
Topic: A combined flow injection/reversed-phase chromatography-high-resolution mass spectrometry workflow for accurate absolute lipid quantification with 13C internal standards
Paper: https://pubs.rsc.org/en/content/articlehtml/2021/an/d0an02443k
Date and time: 20.04.2021, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Andrej
Topic: Hybrid QconCAT-Based Targeted Absolute and Data-Independent Acquisition-Based Label-Free Quantification Enables In-Depth Proteomic Characterization of Wheat Amylase/Trypsin Inhibitor Extracts
Paper: https://pubs.acs.org/doi/full/10.1021/acs.jproteome.0c00752
Date and time: 13.04.2021, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Olya
Topic: LIPIC: An Automated Workflow to Account for Isotopologue-Related Interferences in Electrospray Ionization High-Resolution Mass Spectra of Phospholipids
Paper: https://pubs.acs.org/doi/abs/10.1021/jasms.1c00008
Date and time: 06.04.2021, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Agenda:
1. Overview of XL-MS methods: principles, limitations, software
2. Application
Guest stars: - Alexander von Appen (Alex starts his lab here in a few weeks) and Adrian Nievergelt (Pigino group) - will talk how XL-MS could foster their research
3. Q&A and general discussion
Host: MS Community
Topic: Protein cross-linking
Date and time: 23.03.2021 14:00
Location: ZOOM https://zoom.us/j/5587099875
Host: Olya
Topic: AI-driven Deep Visual Proteomics defines cell identity and heterogeneity
Paper: https://www.biorxiv.org/content/10.1101/2021.01.25.427969v1.full.pdf
Date and time: 16.02.2021, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
Host: Sarita Hebbar (Knust lab) and MS Community
Topic: Dynamic redox balance directs the oocyte-to-embryo transition via developmentally controlled reactive cysteine changes
Paper: https://www.pnas.org/content/pnas/115/34/E7978.full.pdf
Date and time: 02.02.2021, 14:00.
Location: ZOOM https://zoom.us/j/5587099875
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: 26.01.2021, 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 Tkachev, PhD 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 Mitina, PhD 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 | |
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 Events
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: 26.01.2021, 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 Tkachev, PhD 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 Mitina, PhD 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 | |
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
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
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
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
Host: Olya
Topic: Discovering a critical transition state from nonalcoholic hepatosteatosis to nonalcoholic steatohepatitis by lipidomics and dynamical network biomarkers
Paper: https://www.nature.com/articles/s41586-019-1876-xhttps://academic.oup.com/jmcb/article/8/3/195/2588620
Date and time: 15.09.2020, 14:00.
Location: Seminar Room 1, MPI-CBG
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: ZOOM https://zoom.us/j/5587099875
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: ZOOM https://zoom.us/j/5587099875
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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.
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.
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.
2019 Events
Event: X-Mass updates'19
Host: Andrej Shevchenko
Date and time: 17.12.2019, 13:00-17:30
Location: MPI-CBG, Galleria
| 13:00-13:05 | Intro -Andrej Shevchenko- |
| 13:05-13:10 | Knowing each other -introduction round- |
| 13:10-13:40 | LipidXplorer changes... -Jacobo Miranda Ackerman- |
| 13:40-14:10 | Untargeted steroidomics for identifying new adrenal steroids -Paal William Wallace- |
| 14:10-14:40 | Lipotype Shotgun Lipidomics - an update -Christian Klose, Ronny Herzog and Mathias Gerl- |
| 14:40-15:00 | Coffee break |
| 15:00-15:30 | Accelerator mass spectrometry: Detection of "One in a Quadrillion" -Silke Merchel, Johannes Lachner, Georg Rugel, Anton Wallner- |
| 15:30-15:50 | Quantitative Fragmentation Model for Bottom-up Shotgun Lipidomics -Kai Schumann- |
| 15:50-16:20 | Lipid Gold Digger: Building the Shotgun Lipidomics data analysis pipeline -Alessandra Palladini- |
| 16:20-16:50 | Multiomics data integration: Seven layer cake -Canan Has- |
| 16:50-17:30 | Closing remarks -Andrej Shevchenko- |
You are welcome!
2018 Events
Event: X-Mass updates'18
Host: Andrej Shevchenko
Date and time: 18.12.2018, 13:00-16:45
Location: MPI-CBG, Galleria
| 13:00-13:10 | Intro -Andrej Shevchenko- |
| 13:10-13:35 | PeakStrainer & LipidXplorer commercial -Jacobo Miranda Ackerman- |
| 13:35-14:00 | Shotgun Lipidomics Combined with Laser Capture Microdissection -Oskar Knittelfelder- |
| 14:00-14:25 | Lipid markers of psychiatric disorders in blood plasma -Philipp Khaitovich’s lab, SkolTech, Moscow, Russia- |
| 14:25-14:50 | Role of breast milk lipid composition in postnatal brain development -Philipp Khaitovich’s lab, SkolTech, Moscow, Russia- |
| 14:50-15:00 | Coffee break |
| 15:00-15:25 | Lipid Brain Map of human and primates -Philipp Khaitovich’s lab, SkolTech, Moscow, Russia- |
| 15:30-15:55 | LC-MS lipidomics of adipose tissue -Mike Lange- |
| 15:55-16:20 | Organwide mouse lipidomics project -Alessandra Palladini- |
| 16:20-16:45 | Closing remarks -Andrej Shevchenko- |
You are welcome!