VIII Proteomics Workshop Skyline
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The VIII Proteomics Workshop – Skyline will be held by the Brazilian Biosciences National Laboratory (LNBio) at the Brazilian Center for Research in Energy and Materials (CNPEM) Campus in Campinas-SP from 5th to 8th November 2018.
What is Skyline?
Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports all molecules. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.
Why participate?
The course schedule will address emerging quantitative proteomics strategies. This will include the use of Skyline in the context of different quantitative targeted workflows, assay development, generation of acquisition methods, processing of quantitative data sets, as well as using statistical and R software packages and tools in Skyline. Data examples will cover high throughput SRM, MS1 Filtering, parallel reaction monitoring (PRM) and data-independent acquisition (DIA/SWATH). General discussions and strategies of Quantification and statistical processing of acquired data will be discussed during the course.
The instructor list includes international researchers and proteomics experts with a wealth of combined experience in targeted and quantitative proteomics, and both using and creating Skyline applications to meet the needs of his/hers research approach.
This meeting represents a training opportunity for current and future users of the LNBio´s Mass Spectrometry Facility, and researchers in the area of proteomics and mass spectrometry. It also promotes the exchange of scientific information, as well as it motivates the formation of new research groups in the proteomics field.
Following the example of the previous editions, held in the last eight years, the workshop also promotes the exchange of new technologies, the closer relationship between Brazilian and international researchers and dissemination of knowledge in the scientific community.
How much will I invest?
The VIII Proteomics Workshop – Skyline registration fee is mandatory for all participants. The registration fee includes all lectures, conference material, coffee breaks, cocktails and lunches at the event will take place from the 5th until the 8th of November.
Details about the registration and the payment procedures are available in “Applications“.
| VIII Proteomics Workshop Skyline Deadlines | |
| Applications | From September 24th to October 2nd |
| Releasing of shortlisted applicants | October 8th |
| Waiting list call | October 11th |
| Workshop | From 5th to 8th of November |
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In Partnership with
Abstracts book
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Speakers
- Birgit Schilling, Buck Institute for Research on Aging, USA
- Lindsay K. Pino, University of Washington, USA
- Ariel Bensimon, CeMM, Austria
- Christina Ludwig, Technical University Munich, Germany
Program
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Theoretical and Hands-on Program
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Day 1 – 05/11 – Introduction into targeted proteomics – SRM |
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| 8:30 AM | Registration |
| 8:45 AM | Welcome Adriana Franco Paes Leme and Birgit Schilling |
| 9:00 AM | Basics of Quantitative Proteomics – from relative to absolute Tina Ludwig |
| 10:30 AM | Coffee break – Poster presentation 1-12 |
| 11:00 AM | Introduction into targeted mass spectrometry Tina Ludwig |
| 12:00 PM | The biological relevance of targeted proteomics (case study) Ariel Bensimon |
| 1:00 PM | Lunch |
| 2:00 PM | Introduction to Skyline Ariel Bensimon |
| 2:30 PM | Tutorial: SRM method development Tina Ludwig/ Ariel Bensimon |
| 4:00 PM | Tutorial: Data analysis Tina Ludwig/ Ariel Bensimon |
| 6:00 PM | Science Slam – Poster presentation 1-12 (30 min) |
| 8:30 PM | End of day |
Day 2 – 06/11 – Building prior knowledge for targeted proteomics |
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| 9:00 AM | Building prior knowledge for targeted proteomics Birgit Schilling |
| 10:00 AM | Coffee break – Poster presentation 13-24 |
| 10:30 AM | Hands-On: Method refinement Lindsay Pino / Tina Ludwig |
| 12:00 PM | Panorama Introduction and Hands-On: Panorama targeted knowledge base Birgit Schilling |
| 1:15 PM | Lunch |
| 2:15 PM | System suitability and Panorama QC Lindsay Pino |
| 3:30 PM | Coffee break – Poster presentation 13-24 |
| 4:00 PM | Hands-on retention time prediction with iRT in Skyline Ariel Bensimon / Lindsay Pino |
| 6:00 PM | End of day |
| 6:30 PM | Extra time for installation of necessary R scripts and MSstats |
Day 3 – 07/11 – Study design and statistical considerations in targeted proteomics |
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| 9:00 AM | Hands-On: Grouped study data processing with Skyline Ariel Bensimon |
| 10:15 AM | Coffee break – Poster presentation 25-36 |
| 10:45 AM | Study design and statistical considerations Lindsay Pino |
| 12:00 PM | MSstats and its integration with Skyline Lindsay Pino |
| 1:00 PM | Lunch |
| 2:00 PM | Tutorial: MSstats for statistical analysis Lindsay Pino |
| 3:00 PM | Targeting proteomics at high throughput (research examples) Lindsay Pino |
| 4:00 PM | Coffee break – Poster presentation 25-36 |
| 4:30 PM | Waters – The Science of What’s Possible Alexandre Gomes – Mass spectrometry Specialist |
| 4:45 PM | Introduction to Calibration Curves / Absolute Quantification Birgit Schilling |
| 5:15 PM | Hands-On: Calibration Curves / Absolute Quantification Tina Ludwig / Birgit Schilling |
| 6:45 PM | End of day |
Day 4 – 08/11 – Performing PRM and DIA measurements |
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| 9:00 AM | Intro to MS1 Filtering (from DDA data) and from DDA to PRM Birgit Schilling |
| 9:30 AM | Hands-On: MS1 Filtering with Skyline Birgit Schilling |
| 10:30 AM | Coffee break – Poster presentation 37-41 |
| 11:00 AM | Hands-On: PRM with Skyline Birgit Schilling |
| 12:30 AM | Introduction to Data-Independent Acquisition (DIA) Lindsay Pino |
| 1:30 PM | Lunch |
| 2:30 PM | Hands-On: Analysis of DIA data in Skyline Lindsay Pino |
| 4:00 PM | Coffee break |
| 4:30 PM | Future of targeted proteomics Birgit Schilling an all |
| 5:00 PM | Feedback and Course Certificates all |
| 5:30 PM | Kahoot – final quiz and contest all |
| 6:30 PM | End of course |