Thursday, June 28th & Friday, June 29thGel-free Proteomics Data Interpretation, Marc Vaudel & Lennart MartensHands-On Workshop Gel-free Proteomics Data Interpretation: Beautiful Experiments deserve more than the Mascot Summary Gel-free proteomics have the characteristic of producing vast amounts of data: current experiments typically generate hundreds of thousands of spectra themselves containing hundreds of peaks. Before obtaining results from your experiment, it is thus mandatory to conduct a thorough statistical analysis of the data. Hopefully, methods and tools were – and are still being – developed in order to make this task feasible. Moreover, we benefit from numerous online resources making available the proteomic knowledge accumulated along the years. Yet, it is not straightforward to apply these methods in everyday workflows. Even worse, their bad application can simply lead to drawing false scientific conclusions. Also, external resources are often unused, simply because they are unknown. These issues will be addressed in the bioinformatics for proteomics session where we will go through some of the main topics in proteomics data processing in an interactive and user-friendly mode.
a.) 3D structural analysis with a focus on phosphorylation location on the structure Organizers: |
Thursday, June 28th & Friday, June 29thThiol Redox-Proteomics
|
Thursday, June 28th & Friday, June 29thLabel-free LC-MS Quantification
|
Thursday, June 28th & Friday, June 29thDIGE, Barbara Sitek
|
Thursday, June 28th & Friday, June 29th
Spotting Protein Arrays, Caroline May 
Hands-On Workshop: Spotting Protein Arrays
9.00-12.30h / 13.30-17.00
This hands-on workshop will cover the general principles of spotting protein microarrays. The workshop is aimed at proteome-researchers with an interest in immune profiling, spotting and analysis of protein microarrays.
For immune profiling and therefore the discovery of new antibodies, high-density protein arrays are the best alternative approach to ELISAs. A humoral immune response is known to be important in various diseases like autoimmune diseases, infectious diseases or cancer. Therefore antibodies in body fluids, e.g. blood, CSF or also saliva could be good biomarker candidates for the early detection of early onset of the diseases, improving the possibilities for a betimes therapy. Moreover, they can possibly pursue disease progression.
The workshop will cover the following topics:
During the workshop the participants will get an introduction into protein microarray technique, including the analysis of protein microarrays. In the theoretical part a comprehensive overview of different protein microarray applications like e.g. analysis of different body fluids. In the practical part the participants will get an insight into the MPC‘s protein microarray lab performing protein spotting of their own protein microarrays.
- Each participant will receive glas slides for the spotting process and protein soltutions.
- The participants will learn in two groups a spotting workflow.
- In order to be able to examine the biological and technical variance the participants will introduced in different types of analysis software and also our own analysis pipeline. This course is limited to 10 participants.
Organizers:
Caroline May, Immune Proteomics workgroup, Medizinisches Proteom-Center, Bochum
Christian Stephan, Bioinformatics/ Biostatistics workgroup, Medizinisches Proteom-Center, Bochum
Thursday, June 28th & Friday, June 29th
Processing Protein Arrays, Caroline May
Hands-On Workshop: Processing Protein Arrays
9.00-12.30h / 13.30-17.00
This hands-on workshop will cover the general principles of processing protein microarrays. The workshop is aimed at proteome-researchers with an interest in immune profiling, processing and analysis of protein microarrays.
For immune profiling and therefore the discovery of new antibodies, high-density protein arrays are the best alternative approach to ELISAs. A humoral immune response is known to be important in various diseases like autoimmune diseases, infectious diseases or cancer. Therefore antibodies in body fluids, e.g. blood, CSF or also saliva could be good biomarker candidates for the early detection of early onset of the diseases, improving the possibilities for a betimes therapy. Moreover, they can possibly pursue disease progression.
The workshop will cover the following topics:
During the workshop the participants will get an introduction into protein microarray technique, including the analysis of protein microarrays. In the theoretical part a comprehensive overview of different protein microarray applications like e.g. analysis of different body fluids. In the practical part the participants will get an insight into the MPC‘s protein microarray lab performing a differential autoimmune profiling study.
- Each participant will receive two high-density protein microarrays (ProtoArray V.5 sponsored by life technolgies) for autoimmune profiling.
- The protein microarrays will be processed (blocking, incubation with body fluids, washing steps, scanning etc.).
- The protein microarrays of each participant will be compared amongst each other in order to be able to examine the biological and technical variance with different types of commercial software and our own evaluation pipeline.
This course is limited to 10 participants.
Organizers:
Caroline May, Immune Proteomics workgroup, Medizinisches Proteom-Center, Bochum
Christian Stephan, Bioinformatics/ Biostatistics workgroup, Medizinisches Proteom-Center, Bochum
Thursday, June 28th & Friday, June 29th Phosphorylation Analysis, Rene Zahedi
Hands-On Workshop In this hands-on workshop, 4-5 partipants will process samples for phosphoproteomic analyses. Cell lysates will be proteolytically digested and processed, phosphopeptides will be enriched and analyzed by nLC-MS/MS with high mass accuracy. Moreover, participants will learn about current quality control issues in phosphoproteomics such as correct site localization, false discovery rates, and will be introduced to phosphopeptide spectrum interpretation. In addition, quantitative phosphoproteomics strategies, such as iTRAQ, SILAC and SRM will be covered. Topics:
|
