2018 – VIII Proteomics Workshop Skyline

VIII Proteomics Workshop Skyline

Click here to access the Abstracts Book.

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

Supported by


In Partnership with



Abstracts book

Click on the image  to open the complete PDF


  • 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


Theoretical and Hands-on Program


Day 1 – 05/11 – Introduction into targeted proteomics – SRM
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
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
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
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
5:30 PM Kahoot – final quiz and contest
6:30 PM End of course