Mass Spectrometry for Proteomics

The Biomedical Proteomics Research Group

(Planning of the week)

Week is colour coded in to Theory, Practical and theory & Breaks

The attendees will be divided into Group 1 and Group 2 on Tuesday and Wednesday

Assistants during the practical classes are:

Willy Bienvenut - WB

Jennifer Burgess - JEB

Garry Corthals - GC

Carla Pasquarello - CAP

Manfredo Quadroni - MQ

Alexander Scherl - ALS

Monday	Day 1 WB MQ GC CAP
9:30	Welcome Coffee
10:00	Introduction: Perspective of the week and scope of the course WB MQ GC
11:00	Excision of spots from acrylamide gels; start protein reduction WB CAP
12:00	Lunch
13:30	Protein alkylation WB CAP
14:00	Protocol discussion: in-gel digestion CAP
14:30	Washing and destaining of CBB/SS spots WB CAP
15:30	Coffee break
15:45	Introduction to Electrospray and MALDI MS MQ
16:30	Start trypsin digestion WB CAP
17:00	Seminar by Dr Anne Estreicher (SWISS-PROT) group: “Swiss-Prot and other databases, and other things perhaps”

Tuesday	Day 2 GROUP 1 CAP WB GC
8:30	Introduction- program of the day
9:00	Peptide extraction after digestion and deposition on MALDI plate CAP WB GC
9:45	Coffee break
10:00	Sample deposition on MALDI plate and MALDI preparation CAP WB GC
12:00	Lunch
13:30	Packing of micro-HPLC columns GC WB
14:30	MALDI-TOF analysis in detail
15:15	Coffee break
15:30	MALDI-TOF analysis of samples CAP WB GC
17:00	Seminar by Dr Jean-Charles Sanchez: “Applications in biomedical proteomics”

Tuesday	Day 2 GROUP 2 JEB ALS MQ
8:30	Introduction- program of the day
9:00	Peptide extraction; set-up HPLC: solvents, gradients JEB ALS MQ
9:45	Coffee break
10:00	LC-MS: short and long gradients; start samples JEB ALS MQ
12:00	Lunch
13:30	LC-MS: short and long gradients JEB ALS MQ
14:30	LC-MS/MS analysis in detail MQ
15:15	Coffee break
15:30	LC-MS: short and long gradients JEB ALS MQ
17:00	Seminar by Dr Jean-Charles Sanchez: “Applications in biomedical proteomics”

Wednesday	Day 3 GROUP 2 CAP WB GC
8:30	Introduction- program of the day
9:00	Peptide extraction after digestion and deposition on MALDI plate CAP WB GC
9:45	Coffee break
10:00	Sample deposition on MALDI plate and MALDI preparation CAP WB GC
12:00	Lunch Seminar by Dr Manfredo Quadroni: “Chemical protein modification for advance identification”
13:30	Packing of micro-HPLC columns GC WB
14:30	MALDI-TOF analysis in detail
15:15	Coffee break
15:30	MALDI-TOF analysis of samples CAP WB GC
17:00	Tutorial: de novo sequencing

Wednesday	Day 3 GROUP 1 JEB ALS MQ
8:30	Introduction- program of the day
9:00	Peptide extraction; set-up HPLC: solvents, gradients JEB ALS MQ
9:45	Coffee break
10:00	LC-MS: short and long gradients; start samples JEB ALS MQ
12:00	Lunch Seminar by Dr Manfredo Quadroni: “Chemical protein modification for advance identification”
13:30	LC-MS: short and long gradients JEB ALS MQ
14:30	LC-MS/MS analysis in detail MQ
15:15	Coffee break
15:30	LC-MS: short and long gradients JEB ALS MQ
17:00	Tutorial: de novo sequencing

Thursday	Day 4 CAP JEB WB ALS MQ GC
8:30	Introduction- program of the day
9:00	MALDI tools or MSMS software tools CAP JEB WB ALS MQ GC
9:45	Coffee break
10:00	MALDI: data evaluation and analysis WB
12:00	Lunch
13:30	MALDI tools or MSMS software tools CAP JEB WB ALS MQ GC
14:30	LC-MS/MS data evaluation and analysis in detail MQ GC
15:15	Coffee break
15:30	LC-MS/MS data evaluation and analysis in detail MQ GC
17:00	Seminar by Dr Garry Corthals: “Strategies for determination of phosphorylation”

Friday	Day 5 MQ GC CAP
8:30	Introduction- program of the day
9:00	De novo sequencing excesise Theory: instruments and applications MQ GC
9:45	Coffee break
10:00	MS case studies
12:00	Lunch
13:30	roundtable discussion of all experiments AMAP
15:15	Coffee break
15:30	roundtable discussion of all experiments AMAP
17:00	Beer o’clock AMAP