[Arabidopsis] Announcement: Plant Metabolomics and Proteomics Workshop 2011: Mass Spectrometry Informed by Stable Isotope Methods (Free)

Jerry D. Cohen via arab-gen%40net.bio.net (by cohen047 from umn.edu)
Tue Jul 12 17:47:44 EST 2011


Plant Metabolomics and Proteomics Workshop 2011: Mass Spectrometry 
Informed by Stable Isotope Methods

Deadline to apply extended until July 22, 2011

A 'tuition and registration free' educational opportunity:

The other 'omics, metabolomics and proteomics, are powerful tools that
can advance research and offer insights not previously possible.
However, these methods require backgrounds that
are unique from the genomics science they inform.  With the ASPB2011
coming to the Twin Cities this summer, we have a unique opportunity to
share with our colleagues some of the foundations as well as advances
being made by the University of Minnesota group.  Please find the 
announcement through the link at our protein turnover website 
(http://www.proteinturnover.umn.edu/) or you can get it by
direct access at:
http://www.proteinturnover.umn.edu/PMw2011.pdf
This workshop will be held on the University of Minnesota, Saint Paul 
campus just  prior to the ASPB meeting.  The workshop is free and we 
have a very limited number of scholarships also available.  We are 
limited in the number of participants we can handle, so please register 
your interests  early to ensure that we can accommodate your interest. 
Please feel free to circulate this announcement to other interested 
students and colleagues.

....................................................................

Plant Metabolomics and Proteomics Workshop 2011: Mass Spectrometry 
Informed by Stable Isotope Methods

Purpose: To provide
1.	A tutorial on the general workings and application of LC- and GC-mass 
spectrometry in the areas of plant metabolomics and proteomics.
2.	Provide resources (online tools, how to use the MS facility, etc.) to 
lower the barrier for participants to use metabolomics and proteomics 
techniques.
3.	An overview of some specific areas of current metabolomics/proteomics 
research (by showing work being done in our labs).
4.	Hands-on demonstrations of typical metabolomic and proteomic 
workflows (sample collection, extraction, derivatization, isotope 
dilution, analysis)

Lecture topics:
1)	Introduction to Proteomics and Metabolomics: terminology, history and 
general methodology –Hegeman (40+5)
2)	Introduction to separations: Chromatography (GC, LC, 2D-LC, 2D-GC) 
and Electrophoresis SDS-PAGE, 2DGE and CE –Boswell/Cohen (50+10)
3)	Introduction to Mass Spectrometry (instrument types and 		performance 
characteristics) and Interfacing with Separations, (ESI, MALDI, EI) 
introduce imaging -Hegeman/Cohen (50+10)
4)	Proteomics: Workflow, in-gel digests, top down vs. bottom up 
proteomics, Mudpit, Identifying proteins and their modifications, 
database searching and validation, quantification approaches 
–Hegeman/Cohen (50 +10)
5)	Metabolomics: Workflow, sampling and variability, quenching 
metabolism, dealing with chemical diversity, using multiple platforms, 
LC-MS, GC-MS, derivatization, MS/MS, MSn database and computational 
resources – Hegeman/Cohen (40 +5)
6)	Stable isotope methods I. Isotope dilution, protein tagging (ICAT, 
iTRAC, TMT, 18O-water etc.) and tracer techniques –Cohen/Roe (50 +10)
7)	Stable isotope methods II: (Cohen introduce)
a.	Analysis of wine/deuteration of polyphenolics –Roe (25 +5)
b.	Plant hormone analysis by isotope dilution analysis –Xing Liu (25 +5)
8)	Retention projection for metabolite ID –Boswell (50+10)
9)	Metabolomics subtopics: (Hegeman introduce)
a.	Examining the molecular determinants of invasiveness in purple 
loosestrife -Will Menzel (25+5)
b.	Identifying botanical resin sources used by honey bees in propolis 
production –Mike Wilson (25+5)
10)	Stable isotope methods III.  Metabolic labeling methods. Relative 
quantification, Identifying metabolites and using isotopes and MS, 
metabolic flux analysis, partial labeling approaches, labeling mammals – 
Hegeman/Cohen (50 +10)
11)	Protein turnover, discuss history, various labeling approaches for 
analysis of turnover, describe approach for proteome scale turnover 
measurement we have developed –Cohen (40 +5)
12)	Topic to be announced -Bill Gray (50+10)


Hands-on laboratory Modules:
1)	Proteomics fundamentals (Roe, Hegeman and Mike Wilson)
•	Identify an unknown protein!
•	Perform trypsin digestion and solid phase extraction
•	Collect peptide fingerprint and MS/MS data
•	Search data using publicly available search routines
•	We will also provide and discuss in-gel digest protocols
2)	Auxin absolute quantification (Xing Liu)
•	Analysis on GC-QQQ
•	Demonstrate selected reaction monitoring (SRM) approach with GC-MS/MS
•	Quantification by isotope dilution equation
3)	Amino acid analysis via GC-MS (Mary Messner and Justin Settle)
•	Methyl chloroformate derivatization of amino acids from plant samples
•	Analyzed by GC-MS
4)	Demonstration of metabolic labeling approaches (Will Menzel)
•	13CO2 chamber operation and construction
•	learn to grow plants hydroponically for 15N metabolic labeling
5)	Wine analysis, deuteration, and analysis of polyphenolics in 
Minnesota made wines (Roe and Messner)
•	Tasting Monday night (lead by Gary Gardner)
•	LTQ-orbitrap, data preprocessing, elemental composition  (add internal 
standards)
•	Isotope envelope flags polyphenolics in mass spectrum
•	quantification by isotope dilution equation
•	demonstrate volatile trapping with thermal or solvent desorption prior 
to GC-MS (if there is interest)
6)	Metabolic finger printing experiment (Cece Martin and Mike Wilson)
•	Demonstrate experimental design with controls and data collection
•	Discuss data reduction processes and software
•	Statistical analysis: PCA, PLSDA and what it means!
7)	Demonstration of selected ion monitoring (SIM), and reaction 
monitoring approaches (SRM and MRM) for absolute protein or small 
molecule quantification (Boswell)
•	Use the LC-triple quadrupole MS
•	Discuss design of SRM and MRM experiments
•	QConCat strategy for generating labeled standard peptides

After-hours events:
1)	Monday night dinner followed by wine tasting/socializing
2)	Wednesday night drinks and appetizers at Happy Gnome


Workshop 2011 Schedule:
Time	Monday	Tuesday
	Wednesday
	Thursday
	Friday

9 am		LEC1: Introduction	LEC4: Proteomics	LEC7: Stable isotope methods 
part 2	LEC10: Stable isotope methods part 3
9:45 am		LEC2:
Separations	LEC5: Metabolomics	LEC8: Retention Projection	LEC11: Protein 
turnover
10:45am	|	break	break	break	break
11am	Attendees	LEC3: Mass Spectrometry	LEC6: Stable isotope methods 
part 1	LEC9: Metabolomics sub-topics	LEC12:
TBA
12pm	Arrive
|	Lunch	Lunch	Lunch	Closing Remarks/Lunch
1pm		Split into sub-groups and rotate between:	Split into sub- groups 
and rotate between:	Split into sub- groups and rotate between:	Lunch 
cont… Conversation with NSF reps.
2pm		1) MOD 2 or 7	1) finish MOD 1	1) finish MOD 5	
3pm		2) MOD 3 or 4	2) MOD 3 or 4	2) MOD 2 or 7	
4pm				3) MOD 6	
5pm	Sign-in /Welcome!!!	Reunite and start MOD 1	Reunite and start MOD 5		
6-9pm	Dinner + Social Event
	free	Happy Gnome	free	




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