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SMAP Conference, September 19th-22nd 2011, Avignon


Popes' Palace photos credit :
Yann Fareins / Noir d'Ivoire


SMAP Conference, September 19th-22nd 2011, Avignon

Table of contents
General information.....................................................................5
SMAP 2011..................................................................................................6
Organizing committee.................................................................................8
Scientific committee....................................................................................9
Popes' palace plan.....................................................................................12
Practical information.................................................................................14
Oral sessions organisation........................................................................16
Poster sessions organisation.....................................................................17
Exhibitor List..............................................................................................18
Exhibition organisation.............................................................................19

Invited conference.....................................................................................27
Selected short oral communications.........................................................47

Participants list.........................................................................357
Author Index.............................................................................369

SMAP Conference, September 19th-22nd 2011, Avignon



SMAP Conference, September 19th-22nd 2011, Avignon

General information

SMAP Conference, September 19th-22nd 2011, Avignon


SMAP 2011
We are delighted to welcome you to the new SMAP (Mass Spectrometry and Proteomic
Analyses) scientific meeting, which will take place in Avignon, France, from September 19 th to
22nd, 2011. This scientific congress is co-organized by SFSM (Société Française de Spectrométrie
de Masse) and SFEAP (Société Française d'Electrophorèse et d'Analyse Protéomique). The
SMAP2011 congress has for objective to promote scientific disciplines called to play crucial roles
in the XXIth century biology and chemistry. The whole French-speaking scientific community will
exchange in Avignon on federative themes, subjects in emergence and new technological
developments domains related to mass spectrometry and proteomics.

Avignon is one of the most beautiful and famous cities in France
and well-known around the world thanks to the famous song about
the bridge of Avignon. Its beautiful and typically medieval city
center on both banks of the Rhône river attracts millions of tourists
each year. Named the City of the Popes or Altera Roma, Avignon
retains the indelible mark of the Popes’ stay in the city, which was
for a while the capital of the Medieval western world. Today, it is a
prestigious cultural capital with its world-renowned Theatre
Festival. Within a short time, the tourist can visit the most various
sites: Pont du Gard, Nîmes, Arles, the Camargue, Luberon and
Ventoux, Baux de Provence, St Rémy and the Alpilles are close to
the town. The variety of attractions and sites to visit can enrich
your trip to Provence. The era of the Popes somewhat eclipses
other events in what is a long and tumultuous history. At the
crossroads of the big trade and migratory routes between northern
and southern Europe and between Italy and Spain, the city played a
major role in European history. A Phoenician trading post during
the High Antiquity, Avignon then became a flourishing Roman
town. It suffered greatly from the barbarian invasions, followed by
those of the Moors and the Francs in the High Middle Ages. With
the expansion of trade, and benefiting from its strategic position
and its bridge over the Rhône, it had the status of a free town,
strong and arrogant enough to defy the King of France. The
presence of the Popes made Avignon the capital of the Medieval
western world in the 14th century. A papal territory up until the French Revolution, the city
actually benefited little from the first Industrial Revolution. It entered into relative anonymity in
the 19th century only to come back as a cultural capital in the 20th century. Avignon is the cradle
of the Félibrige, a revival of Provençal literature and its Theatre Festival, started in 1946 by Jean
Vilar, gives it international prestige.
During the 14th century, the city of Avignon was part of the Pontifical States, and as such was
sheltered from war and destruction. Since the High Middle Ages, Avignon has been a vital
intellectual and commercial cross-road in Europe, a choice location for exchange, meetings and
discussions. Today, its internationally-known cultural influence and attraction have made it one


SMAP Conference, September 19th-22nd 2011, Avignon

of the most prestigious conference sites in the world. The International Congress Center was
created in 1976 within the outstanding premises of the Palace of the Popes and hosts many
events throughout the entire year. The Congress Center, designed for conventions, seminars,
and meetings, now occupies two wings of the Popes’ Palace. The Jeanne Laurent Building, an
outlying building just outside the Popes’ Palace Congress Center, is located in the former papal
gardens and can host working meals or exhibits relating to congresses held in the Congress
Center. The Jeanne Laurent building is made up of four vaulted rooms in exposed stone, with
magnificent views over the Rhône river, offering a splendid panorama of the Rhône Valley.

SMAP Conference, September 19th-22nd 2011, Avignon


Organizing committee
Jean Armengaud1
Alain Dedieu1
Christian Godon1
Véronique Malard1
Olivier Pible1
Jean-Charles Gaillard1
Philippe Guérin1
Céline Bland1
Béatrice Alonso1
Anne-Hélène Davin1
Nicole Sage1

Jérôme Garin2
Christophe Bruley2
Myriam Ferro2
Damien Barthe2
Véronique Dupierris2
Annie Adrait2
Alexandra Kraut2
Sabine Brugière2
Céline Fleury2
Marie Arlotto2
Mathieu Baudet2
Yves Vandenbrouck2


Laboratoire de biochimie des systèmes perturbés (LBSP),
Institut de biologie environnementale et biotechnologie (IBEB)
Direction des sciences du vivant (DSV)
Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), BP17171,
30207 Bagnols-sur-ceze


Etude de la Dynamique des Protéomes (EDyP)
Laboratoire Biologie à Grande Echelle (BGE)
Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV)
Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA),17 rue des
Martyrs, 38054 Grenoble


SMAP Conference, September 19th-22nd 2011, Avignon

Scientific committee

Marc Bonneu, Plateforme Proteome, Centre de Génomique Fonctionnelle Bordeaux, 146 rue
Léo Saignat, F-33076 Bordeaux Cedex

Julia Chamot-Rooke, Laboratoire des Mécanismes Réactionnels, CNRS UMR 7651, Ecole
Polytechnique, 91128 Palaiseau Cedex

Philippe Dugourd, Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579
CNRS/Université Lyon 1, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex

Jérôme Garin, Laboratoire Biologie à Grande Echelle (BGE), U1038 INSERM/CEA/UJF, CEA), 17
rue des Martyrs, F-38054 Grenoble Cedex,

Bruno le Bizec, LABERCA - U1329 INRA, Ecole Nationale Vétérinaire, Agroalimentaire et de
l’Alimentation Nantes Atlantique (ONIRIS), Atlanpôle – Site de la Chantrerie - BP 50707, F-44307
NANTES Cedex 3

Philippe Marin, Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U661,
Universités Montpellier I & II, 141, rue de la Cardonille, F-34094 Montpellier Cedex 5

Charles Pineau, INSERM U625, Proteomics Core Facility Biogenouest, Campus de Beaulieu,
Université de Rennes I, F-35042 Rennes, France

Michel Salzet, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée
(FABMS), EA 4550, IFR 147, Cité Scientifique, Université Lille Nord de France, Lille 1, 59650
Villeneuve d'Ascq

SMAP Conference, September 19th-22nd 2011, Avignon




SMAP Conference, September 19th-22nd 2011, Avignon

SMAP Conference, September 19th-22nd 2011, Avignon


Popes' palace plan

1-Salles des Gardes : Welcome / Informations / Registration
2-Cellier Benoit XII : Oral conferences (even number) & Manufacturer conferences
3-Paneterie : Poster sessions n°1 & n°2
5-Conclave : Plenary conferences & Oral conferences (odd number)
7-Chambre du trésorier : Manufacturer conferences
9-Herses Champeaux : SFEAP & SFSM Young
12-Grande audience : Exhibitors room & Coffee breaks
13-Espace Jeanne Laurent : Lunch & Gala dinner


SMAP Conference, September 19th-22nd 2011, Avignon

1-Salles des Gardes : Welcome /
Informations / Registration

2-Cellier Benoit XII : Oral conferences
(even number) & Manufacturer conferences

3-Paneterie : Poster sessions n°1 & n°2

5-Conclave : Plenary conferences &Oral

7-Chambre du trésorier : Manufacturer

12-Grande audience : Exhibitors room &


SMAP Conference, September 19th-22nd 2011, Avignon

conferences (odd number)

Coffee breaks


Practical information
Office hour of desks
Please collect your satchel, program book,
name badge from the registration desk. The
registration desk will open at the «Salle des
Gardes» :
• Monday 19 September, 2 pm - 7 pm
• Tuesday 20 September, 8 am - 6:30 pm
• Wednesday 21 September, 8 am - 6:30 pm
• Thursday 22 September, 8 am - 4 pm
Official language
The official languages of the congress are
English and French according to the laws of the
French republic on the use of the French
language. The oral communications and the
posters can be in French, in that case, their
summary and title are presented in French in
the program and the book of summaries.
Voluntaries will be at your disposal to welcome
you, guide you in the center of the Popes'
Palace Conference Center, during the sessions
and the excursions. Do not hesitate to seek
them, they are recognizable in their T-shirt
with the logo of the SMAP2011 Avignon
For security and regulation reasons, please
wear your name badge at all times. It is your
admission to all sessions, breaks in the
"Grande Audience" room, lunches in Jeanne
Laurent Building.

Cellular phones
Cellular phones must be switched off in the
conference rooms.
Lost and Found
For lost and found personal belongings, please
contact the information desk in the «Salle des
First Aid
In case of emergency, please, contact the
information desk in the «Salle des Gardes».
Under this phone number you can reach the
desk at all office hours : +33 490 27 51 50.
Please feel welcome to provide the Local
Organizing Committee with any feedback
or to ask for clarification of any information.
• Registration queries, please contact Ms.
Céline Gallard by email c.gallard@palaisdes-papes.com or phone +33 490 27 50 57
• Scientific queries, please contact Mr Jean
Armengaud or Mr Jérôme Garin by email,
respectively jean.armengaud@cea.fr and
Please remember that smoking is not allowed
in the congress center.
Wireless connexion will be available in
«Grande audience» and «Salle des gardes»

Coffee breaks
Morning and afternoon coffee breaks will be
served only in the «Grande Audience» room. Changing room
Participants are not allowed to carry out drinks A changing room will be open throughout the
conference in the main entrance near the
or food in working rooms.
«Salle des gardes». It will be possible to store
luggage in this changing room area.
Please, note that there will be no exchange
facilities at the International Conference Toilets
Center. Lots of banks are present in Avignon They are situated near the «Salle des Gardes»,
center all around the Popes’Palace Conference between the «Paneterie» and The «Conclave»
hall, in «Jeanne Laurent» Building and near the
«Grande Audience».


SMAP Conference, September 19th-22nd 2011, Avignon

SMAP Conference, September 19th-22nd 2011, Avignon


Oral sessions organisation
They will occur in the room of Conclave and Cellier Benoit XII (respectively n°5 and n°2 on the
plan page 12).

Instructions for oral communication
• Short oral presentations will be strictly limited to 15 minutes. A 5-minute period

between presentations will accommodate questions, discussion, and introduction of
the next speaker. This 5-minute period belongs to the audience and to the chairs of the
Microsoft PowerPoint and Adobe Acrobat Reader are the only acceptable audiovisual
formats for electronic presentations. Accepted formats are: .ppt, .pps or .pdf. The
venue will be equipped with a dedicated PC laptop operated under windows. Please,
bring your presentation on a Flash drive.
Uploading your presentation should be done preferentially once you register for the
SMAP meeting upon your arrival in “Salles des Gardes”. You should upload your
presentation either the day before for an oral presentation in the morning or in the
morning if your presentation is scheduled in the afternoon.
Please, be present in the conference room 15 min before the beginning of your
session in order to have time to discuss with the session chair that will be in charge to
introduce you.
We recommend to all speakers to have all their slides in English as a courtesy for our
foreign guests. Oral presentation of your talk in English will be appreciated.

Organisation des conférences
Elles se dérouleront dans les salles du Conclave et Cellier Benoit XII (respectivement n°5 et n°2
sur le plan page 12).

Instructions pour les conférences sélectionnées

• Durée des présentations : 15 min précisément et 5 min gérées par le modérateur


permettant des questions / discussions et l’introduction de l’orateur suivant. Compte
tenu de la configuration du centre des congrès et de la circulation entre les salles en
session parallèle, les horaires seront strictement respectés.
Fichier : Les présentations doivent être faites sous Powerpoint ou Adobe Acrobat
Reader. Fichiers acceptés : .ppt, .pps ou .pdf. Le PC de projection sera sous Windows.
Apportez votre présentation sur clé USB.
Remise des fichiers : ils devront être remis de préférence au moment de votre
enregistrement à l’accueil du palais des Papes (Salle des Gardes). En dernier recours :
la veille si votre conférence est le matin ; le matin si votre conférence est l’après-midi.
Etre présent 15 min avant le début de votre session dans la salle où se déroulera celleci afin de rencontrer le modérateur en charge d’introduire votre présentation.
Nous recommandons à tous les conférenciers de présenter l’ensemble de leurs
diapositives en anglais par courtoisie auprès de nos invités anglophones. La
présentation orale de vos travaux en anglais serait très appréciée.

SMAP Conference, September 19th-22nd 2011, Avignon

Poster sessions organisation
There will be two poster sessions, both will be in the Paneterie room (n°3 on the plan, page 12).

Session n°1 : Poster P1 to P134

Session n°2 : Poster P135 to P268
Display : poster should be mounted :

Session n°1 : From tuesday 20 september before 8:30am, till wednesday 21
september 12:00am.
At the end of session n°1, posters will be removed to give way to those of session n°2,

Session n°2 : From wednesday 21 september before 1:30pm till thursday 22
september 3:30pm.

Organisation sessions posters

Il y aura deux sessions poster, les deux se tiendront dans la salle Paneterie (n°3 sur le plan page

Session n°1 : Poster P1 à P134

Session n°2 : Poster P135 à P268
Affichage : votre poster devra être mis en place :

Session n°1 : Le mardi 20 septembre avant 8h30 jusqu'au mercredi 21 septembre
A la fin de la session n°1 les posters seront enlevés pour faire place à ceux de la session

Session n°2 : Le mercredi 21 septembre avant 13h30 jusqu'au jeudi 22 septembre

SMAP Conference, September 19th-22nd 2011, Avignon


Exhibitor List




Mr Jean- Baptiste VINCENDET
Mr ees VLAK

Mr Frédéric METRAL


Mr Lionel Chauvin
Mr Sergio MELIS
Mr Guillaume CHARLOT

Mr Patrick VESCOVI


Mr Valentin BOUQUET
Mr Frédéric VIART




Mr Stéphane FESSEMAZ

Mrs Agnès CORBIN



Mr Julien GUERIN

Mrs Chirstine HERR

Mr Thierry SALOMON

Mr Nicolas RAYNAL




Mrs Karima BAUDIN
Mr Christophe CLARYSSE


Mr Emmanuel CRENN

Mrs Christine AYOUB

Ms Jana LEE


Mrs Catherine BALTHASAR

Mr Philippe BOGARD




Mr Markus KOLBE
Dr Martin LINKE


Mr Claude NETTER

Mr Mikael LEVI
Mr Stéphane MOREAU



Mrs Fabienne PALGE

Mr Christophe DABADIE
Mr Jocelyn DUPUY
Mr Etienne MAOUT
Mrs Madeleine PEYTAVIN




Mr Jean- Louis SCHAFFAR

16 - F-DBS


Mrs Sophie BERTAUX


Mr Akihiko KUSAI
Mr Jean- Pierre MUNIER


SMAP Conference, September 19th-22nd 2011, Avignon

Exhibition organisation
In Grande Audience room
(n°12 on plan page 12)

SMAP Conference, September 19th-22nd 2011, Avignon



SMAP Conference, September 19th-22nd 2011, Avignon

- Codes in square brackets are the abstracts' identifiers :
•[Ix] are for « Invited » conferences
•[Ox] are for selected Oral conferences
- Numbers in brackets next to room name refering to popes' palace plan, page 12.

Monday September 19th

Petite Cuisine (16)

Training day
Imagerie MALDI-TOF : des drogues aux protéines


Salle des gardes (1)

Conferee check-in


Herses-Champeaux (9) SFEAP & SFSM Young


SFSM & SFEAP presidents' welcome word


Opening conference 1
Graham COOKS
Ambient Ionization and Miniature Mass Spectrometers

Conclave (5)

Opening conference 2
Proteomics analyzes reveal unexpected aspects of the
evolution of phagosomes over 1.2 billion years [I8]


Grande Audience (12)



Cocktail & Inauguration Exposition
Private guided tour of the Popes' Palace

SMAP Conference, September 19th-22nd 2011, Avignon


Tuesday September 20th

Conclave (5)


Session 1 - System's Biology


Conclave (5)

Paneterie (3)
Grde Audience (12)


Conclave (5)

Régis Lavigne - Systems analysis
fermentation and respiration [O25]



Break :
Poster session n°1
Coffee & Exposition

Gérémy Clair - System biology insights into the global
remodeling of proteome and pathogenicity of Bacillus cereus
induced by oxydoreduction potential [O32]

Session 2 - Imaging & Mobility


Jennifer BRODBELT - Development and Applications of
Photodissociation for Biological Applications [I4]
Cellier Benoit XII (2)

Paneterie (3)
Grde Audience (12)

Grégory Hamm - Développement Méthodologique pour la
Quantification en Imagerie par Spectrométrie de Masse (qMSI)
Break :
Poster session n°1
Coffee & Exposition
Daniel Lafitte - Quelle voie pour la caractérisation d’ isoformes
protéiques sur coupe de tissu par MALDI in source decay ?

Cellier Benoit XII (2)


Claudia Bich - Compatibilité entre histologie et imagerie par
spectrométrie de masse ToF-SIMS : détection et cartographie
de lipides au sein de tissus biologiques [O5]
Patrice Garcia - Détection de l’epo humaine recombinante
dans les fluides biologiques equins par LC-MS/MS [O34]


Jeanne Laurent (13)



Cellier Benoit XII (2)

Manufacturer conference : Agilent


Chbr du Trésorier (7) Manufacturer conference : AB Sciex


Grde Audience (12)



Bertrand Fabre - Characterization of cellular proteasome
complexes diversity by proteomic approaches [O13]



Paola PICOTTI - Targeted proteomics from proteins to
proteome maps : potential and bottlenecks [I16]

Hans C. Hürlimann - Using proteomics to identify AICAR
cellular targets [O27]



Plenary conference 1 - Anne-Claude GAVIN - A systematic
screen for protein–lipid interactions in Saccharomyces
cerevisiae [I10]


SMAP Conference, September 19th-22nd 2011, Avignon

Tuesday September 20th

Conclave (5)


Session 3 - Instrumentation



Perdita BARRAN - Ion Mobility Mass Spectrometry for
Intrinsically Disordered Proteins a SWOT analysis [I2]
Conclave (5)

Paneterie (3)
Grde Audience (12)



Quentin Enjalbert - Photo-SRM: laser photo-dissociation
improves detection selectivity of selected reaction monitoring
mode [O7]
Break :
Poster session n°1
Coffee & Exposition
Mathieu Dupré - LDI-MS of proteolytic synthetic model
peptides deposited on silicon-based nanowires: an alternative
to MALDI PMF? [O17]

Conclave (5)


David Touboul - ETD à pression atmosphérique [O6]
Marion Girod - Optical profiling of an Agilent Jet Stream
Technology electrospray by Laser-Induced-Fluorescence
coupled to mass spectrometry measurements [O14]


Session 4 – Proteome Dynamics


Cellier Benoit XII (2)

Christopher OVERALL - Traveling to the Ends of the Proteome
World. Positional N-terminal and C-terminal proteomics
deciphers protein terminal and proteolytic post-translational
modifications in the HPP [I15]
Catherine Moali - Use of quantitative proteomics to study
function and specificity of an emerging protease family in cellbased assays [O22]

Paneterie (3)
Grde Audience (12)


Plenary conference 2 - Martin JARROLD - Charge Detection
Mass Spectrometry [I12]

Break :
Poster session n°1
Coffee & Exposition
Anne Gonzalez de Peredo - Evaluation of label-free
quantitative proteomic methods together with sample
fractionation for the large-scale analysis of inflammatory
endothelial cells [O18]

Cellier Benoit XII (2)


Joseph Gault - Post Translational Modifications and
Pathogenesis of Bacterial Meningitis Is a «one shot» Approach
for Complete Mapping Realistic? [O37]
Pascal Seyer - Identification and characterization of new
protein partners of serotonin transporter [O29]


Cellier Benoit XII (2)

Manufacturer conference : Thermo


Chbr du Trésorier (7) Manufacturer conference : Waters

SMAP Conference, September 19th-22nd 2011, Avignon


Wednesday September 21st

Conclave (5)

Plenary conference 3 - Guy BOUCHOUX - From the mobile proton
to wandering hydride ion: some mechanistic aspects of gas-phase ion
chemistry [I3]


Session 5 - FT-ICR, Complexes



Christian ROLANDO - Two dimensional FT-ICR, the only way to obtain
Conclave (5)

all the MS/MS correlations from a sample without selecting the parent
ions. Instrumental developments and analytical applications [I17]

Carlos Afonso - Identification par très haute résolution FT-ICR de
processus induits par la charge dans la décomposition de peptides
cycliques en ECD [O33]


Paneterie (3)
Grde Audience (12)


Break :
Poster session n°1
Coffee & Exposition
Edith Nicol - Mechanisms leading to unusual ECD fragments: the ion
spectroscopy perspective [O11]


Conclave (5)


Sébastien Schramm - Tabagisme actif/tabagisme passif, une étude
différentielle de la fraction particulaire [O15]

Elisabetta Boeri Erba - Quantifying Protein-Protein Interactions
Within Noncovalent Complexes Using Electrospray Ionization Mass
Spectrometry [O3]


Session 6 - Proteomics & Health


Bruno DOMON - A Novel Strategy in Quantitative Proteomics: Its
Implication for Biomedical Research [I9]


Cellier Benoit XII (2)

Christophe D. Masselon - Bladder Cancer Biomarker Candidates
Discovery in a Multi-site Patients Cohort: a Label-free Quantitative
Proteomics Study [O38]

Grde Audience (12)

Break :
Poster session n°1
Coffee & Exposition
Willy V. Bienvenut - Proteomic targeting of angiogenic cell lines by
fumagillin mostly relies on the expression levels of METAP1 [O16]


Cellier Benoit XII (2)


Yannick Charretier -Microorganism characterization for the clinics
using SRM [O19]

Jérôme Chenau - Détection sensible et spécifique des spores de
Bacillus anthracis dans des matrices environnementales
immunocapture et spectrométrie de masse en mode MRM [O28]


Poster session n°1 taking down / Poster session n°2 hanging up

Jeanne Laurent (13)



Cellier Benoit XII (2)

Manufacturer conference : Bruker


Chbr du Trésorier (7) Manufacturer conference : Advion


Chbr du Trésorier (7) Manufacturer conference : Promega


Grde Audience (12)



SMAP Conference, September 19th-22nd 2011, Avignon

Wednesday September 21st

Conclave (5)


Session 7 - Signaling


Plenary conference 4 - Seth Grant - The organization of
synapse proteomes [I11]

Conclave (5)

Paneterie (3)
Grde Audience (12)

Sacha BAGINSKY - Functional Proteomics: A Cornerstone in
Plant Systems Biology [I1]
Sonia Hem - Targeted proteomics profiling of the plasma
membrane transportome in Arabidopsis thaliana [O20]
Break :
Poster session n°2
Coffee & Exposition
Franck Vandermoere - A quantitative phosphoproteomic approach
reveals differential phosphorylation of serotonin 2a receptor upon
activation by hallucinogenic versus non-hallucinogenic agonists [O1]

Conclave (5)

Sonia Cantel - Reflectron Positive ion Mode Matrix-Assisted
Laser Desorption/Ionization Mass Spectrometric Analysis of
Sulfo-peptides [O8]


Session 8 - Fragmentation


Cellier Benoit XII (2)


Jordane Biarc - The Induction of Serine/Threonine Protein
Phosphorylations by Native and Mutant PDGFR/TrkA Chimeras
in Stably Transfected PC12 Cells [O2]

Yury TSYBIN - Traveling to the Ends of the Proteome World.
Positional N-terminal and C-terminal proteomics deciphers
and proteolytic
modifications in the HPP [I18]
Emmanuelle Sachon - Effets de l’acétylation des peptides de la
peau de la rainette Pachymedusa dacnicolor pour un
séquençage de Novo par MALDI-TOF/TOF [O21]

Paneterie (3)
Grde Audience (12)


Break :
Poster session n°2
Coffee & Exposition
Corinne Buré - Structure Determination of Complex Plant
Glycosphingolipids by Tandem Mass Spectrometry [O4]

Cellier Benoit XII (2)

Stéphane Bouchonnet - Investigating the unusual behavior of
Metolachlor under chemical ionization in hybrid ion trap mass
spectrometry [O12]
Thierry Fouquet - Analytical strategy combining NMR, chemical
synthesis and mass spectrometry for molecular and structural
characterization of plasma-polymerized siloxanes [O23]


Cellier Benoit XII (2)

SFSM Meeting


Chbr du Trésorier (7) SFEAP Meeting


Jeanne Laurent (13)

Gala dinner

SMAP Conference, September 19th-22nd 2011, Avignon


Thursday September 22nd

Conclave (5)


Session 9 - Bioinformatics


Oliver KOHLBACHER - Automated high-throughput analysis of
quantitative proteomics data [I14]
Conclave (5)

Paneterie (3)
Grde Audience (12)

Conclave (5)

Break :
Poster session n°2
Coffee & Exposition

Benoit Valot - Nouveaux algorithmes de regroupement pour
gérer l'identification des protéines ou de modifications posttraductionnelles dans les analyses de protéomique à haut
débit [O36]
Session 10 - Metabolomics

Cellier Benoit XII (2)

Paneterie (3)
Grde Audience (12)


Christine Carapito - Une suite logicielle pour la protéomique
interfacée sur une grille de calcul. Utilisation d'algorithmes
libres pour l'identification MS/MS, le séquençage de novo et
l'annotation fonctionnelle [O30]

Markus Muller - Evaluating the accuracy of the positioning of
phosphorylations by MS/MS spectra [O24]



Plenary conference 5 - Olga VITEK - Statistical methods and
tools for protein quantification in MS-based proteomics [I19]

Cellier Benoit XII (2)

Pascal KINTZ - Mass spectrometry in forensic hair testing :
example of drug-facilitated crimes [I13]
Emilien Jamin - Développement d’une méthode
métabolomique associant la RMN et l’UHPLC-HRMS [O9]


Break :
Poster session n°1
Coffee & Exposition
Sylvain Chéreau - Prises d’empreintes urinaires par LC-HRMS :
La métabolomique, une stratégie innovante pour le dépistage
de l’utilisation d’anabolisants en élevage [O10]
Agnéta Kiss - L’apport de la spectrométrie de masse haute-résolution à
l’obtention d’empreintes moléculaires d'échantillons d’urine. Applications
potentielles au dopage [O35]


Jeanne Laurent (13)



Plenary conference 6 - Virginie BRUN
PSAQ standards for accurate quantification of proteins: from
the concept to clinical application [I5]

Conclave (5)

SFSM / SFEAP prizes


Closing conference - Pierre CHAURAND
MALDI Imaging Mass Spectrometry: Principle, State of the Art
and Future Challenges [I6]




SMAP Conference, September 19th-22nd 2011, Avignon

Invited conference

SMAP Conference, September 19th-22nd 2011, Avignon


[I1] Functional Proteomics: A Cornerstone in Plant Systems Biology
Martin-Luther-Universität Halle-Wittenberg, Institut für Biochemie und Biotechnologie,
Abteilung Pflanzenbiochemie, Weinbergweg 22 (Biozentrum), 06120 Halle (Saale),
Contact : sacha.baginsky@biochemtech.uni-halle.de

Different functional proteomics tools are now available that enable the quantitative
characterization of proteome dynamics and the mapping of posttranslational modifications. We
report here examples how we used these tools to characterize the functional proteome of
Arabidopsis and rice cell organelles, with a focus on plant-specific plastids. We analyzed the
Arabidopsis proteome at genome-scale and provide quantitative information about organellar
proteomes in different plant organs by «normalized spectral counting» (Baerenfaller et al.,
Science 320, 938-41; Baerenfaller et al., Integrative Biology 3, 225-237). For a functional
characterization of plastid protein import, we analyzed the proteomes of protein import
mutants and established protein N-termini to distinguish precursor from mature plastid
proteins in WT, ppi1 and ppi2. These analyses revealed the accumulation of precursor proteins
in the cytosol of protein import mutants. In order to assess the short-term regulation of the
chloroplast proteome in response to environmental signals, we analyzed the chloroplast
phosphoproteome and characterized its dynamics during a circadian cycle (Reiland et al., Plant
Physiol. 150, 889-903). Phosphorylation motif utilization suggests that the phosphorylation
network topology in chloroplasts is characterized by many-to-many relationships. To establish
the kinase/substrate nodes in this network we performed comparative quantitative
phosphoproteome profiling experiments with wildtype and kinase mutant plant material,
starting out with the STN8 kinase. Differential protein phosphorylation was assessed by relative
quantification with «extracted ion chromatograms» and the data were further validated by
functional characterization of selected substrates (Reiland et al., Proc. Natl. Acad. Sci. USA, in
press). We present here our data, comment on reliability and reproducibility and propose
strategies to increase both at a reasonable cost.


SMAP Conference, September 19th-22nd 2011, Avignon

[I2] Ion Mobility Mass Spectrometry for Intrinsically Disordered Proteins a SWOT
Perdita BARRAN
The EastChem School of Chemistry, The University of Edinburgh, Edinburgh, UK
Contact : perdita.barran@ed.ac.uk

The p53 protein is a transcription factor which plays a central role to tumour
suppression. Loss of p53 function is correlated with the development of cancer in which the
MDM2 protein binds to the N-terminal transcription activation domain shutting down function 3.
Mass spectrometry studies of WT p53 and mutants of the DNA binding domain following nanoelectrospray from native conditions show a wide charge state range for charge states n= 8 - 18
for monomeric species of the general form [M+nH] n+. Mass spectrometry data from both
instruments are qualitatively similar. The most abundant peaks are at n =9 and n=10 indicating
the dominance of a compact structure. Multimeric species are observed for the WT and
mutants, however the dimers shown in the WT are more intense. Generally, the collision crosssections of the monomer are observed to increase with increasing charge in a stochastic fashion
attributed to protein unfolding due principally to coulombic repulsion, which can be attributed
to the ‘plasticity’ of these IDP’s . Multiple gas-phase conformers are resolved for a number of
charge states, over a very wide charge state range. Subtle differences in unfolding transitions
between the WT and mutated samples can be characterized. For instance the H115N mutant,
altered at the boundary of loop I seems to be less structured – favoring the more extended
conformations when compared with WT p53.,Conversely, the R249A/H115N mutant appears to
be more compact. The thermally induced unfolding also shows interesting trends, and in
particular reveals the resistance to unfolding of this important IDP. These results are interpreted
in terms of the biological activity of these proteins and also in terms of the implications for the
use of IM-MS to study this largely ignored, but critically important, class of proteins.

SMAP Conference, September 19th-22nd 2011, Avignon


[I3] From the mobile proton to wandering hydride ion: some mechanistic aspects of
gas-phase ion chemistry
Ecole Polytechnique, Laboratoire des Mécanismes Réactionnels (DCMR), Département
de Chimie, 91120 Palaiseau, France; CNRS, UMR 7651, Palaiseau Cedex, France
Contact : bouchoux@dcmr.polytechnique.fr

Structural characterization of molecular species by mass spectrometry supposes the knowledge
of the type of ions generated and the mechanism by which they dissociate. In this context, a
need for a rationalization of ESI(+)(-) mass spectra of small molecules has been recently
expressed [1]. Similarly, at the other end of the mass scale, efforts are currently made to
interpret the major fragmentation processes of protonated and deprotonated peptides and
their reduced forms produced in electron capture (ECD) or electron transfer (ETD) experiments
Most fragmentation processes of molecular and pseudo-molecular ions may be described by a
combination of several key mechanistic steps: simple bond dissociation, hydrogen atom,
hydride ion or proton migrations, formation of ion-neutral complex intermediates… Selected
crucial aspects of these elementary reactions, occurring inside positively charged ions, will be
recalled and illustrated by examples taken in the recent mass spectrometry literature. Emphasis
will be given on the protonation process and its consequences in term of structure and
energetic [4].
1 – WMA. Niessen. Mass Spectrom Rev 2011, 30, 626-663.
2 – AG Harrison. Mass Spectrom Rev 2009, 28, 640-654.
3 – SA McLuckey, M Mentinova. J Am Soc Mass Spectrom 2011, 22, 3-12.
4 – G Bouchoux. Mass Spectrom Rev 2007, 26, 775-835.


SMAP Conference, September 19th-22nd 2011, Avignon

[I4] Development and Applications of Photodissociation for Biological Applications
Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX
Contact : jbrodbelt@mail.utexas.edu

The tremendous growth in the application of mass spectrometry for detection, quantification
and characterization of biological molecules has spurred the exploration of new ion
activation/dissociation methods. Although collision induced dissociation (CID) remains the gold
standard for structural characterization of ions, it has several shortcomings (e.g. insufficient
energy deposition, limited applicability for pinpointing post-translational modifications in
peptides, etc.) that have stimulated the search for other activation methods. Photodissociation
offers an especially promising alternative to traditional CID in ion traps, in addition to its success
with FTICR and time-of-flight instruments.
There are several compelling advantages of using lasers to activate ions in a mass spectrometer.
Photoactivation is a non-resonant process, meaning that both the selected precursor ions and
primary fragment ions may be activated, leading to secondary dissociation and a richer array of
fragment ions without requiring deliberate sequential stages of ion manipulation. The ability to
vary energy deposition without resorting to multi-stage experiments (MS n) is particularly
important when analyzing macromolecules in which initial ion currents may be low and the total
sample quantity is limited.
The reduction of ion losses is a critical feature when analyzing small ion populations while
maintaining adequate detection sensitivity. Photoactivation can be utilized to analyze both
negative and positive ions, so it offers the potential for broader characterization of the
proteome. UV photodissociation using a laser offers fast, high energy deposition that yields
good sequence coverage for peptide analysis.

SMAP Conference, September 19th-22nd 2011, Avignon


[I5] PSAQ standards for accurate quantification of proteins: from the concept to
clinical application
Virginie BRUN
Laboratoire d'Etude de la Dynamique des Protéomes, Unité de Biologie à Grande
Echelle, CEA/INSERM/UJF 1038, 17, rue des Martyrs, 38054 cedex 9 Grenoble, France
Contact : virginie.brun@cea.fr

Technological developments that will provide reliable and multiplex quantification of proteins in
biofluids are critical for biomarker research and medical science. Mass-spectrometry analysis is
currently attracting considerable interest due to its multiplexing capacities. Combined with
stable isotope-labelled quantification standards [1], MS-based assays can provide quantitative
data for hundreds of peptides generated by trypsin digestion of proteins. However, to envision
MS as a relevant methodology for biomarker evaluation and biomarker measurement in clinical
laboratories, some analytical variabilities still need to be resolved [2].
In 2007, we developed the PSAQ TM method (Protein Standard Absolute Quantification) which
uses full-length isotope-labelled protein standards to quantify target proteins [3]. In this
presentation, we’ll demonstrate the specific advantages of the PSAQ TM method for accurate
and reliable quantification of protein biomarkers. Recent technological advances related to the
production and use of PSAQ TM standards will be presented. Several applications of the PSAQ TM
method in the health domain will also be exposed.
1. Brun V. et al., (2009) Isotope dilution strategies for absolute quantitative proteomics. J.
Proteomics 72, 740-749.
2. Hoofnagle A.N. et al., (2010)Quantitative Clinical Proteomics by Liquid ChromatographyTandem Mass Spectrometry: Assessing the Platform. Clin. Chem. 56, 161-164.
3. Brun V. et al (2007) Isotope-labeled protein standards: toward absolute quantitative
proteomics. Mol. Cell. Proteomics 6, 2139-2149.


SMAP Conference, September 19th-22nd 2011, Avignon

[I6] MALDI Imaging Mass Spectrometry: Principle, State of the Art and Future
Département de chimie, université de Montréal. Montréal, Québec, Canada
Contact : pierre.chaurand@umontreal.ca

MALDI-based imaging mass spectrometry is a new technology that allows to
map different biocompounds and xenobiotics directly from thin tissue sections. Numerous
classes of biomolecules including metabolites, phospholipids, peptides and proteins can be
detected and mapped in direct correlation with the underlying histology. Molecular profiles and
images depend on the types of tissues or cells studied and certain signals can be directly
correlated with the health status of the tissue specimen. Indeed, the technology is sufficiently
sensitive to detect variations in the molecular composition induced by the presence of disease
or by drug uptake. Numerous technical advances such as automated matrix deposition and the
development of in situ chemistries now allow us to study the proteomic content of fresh frozen
and formalin fixed paraffin embedded tissue specimens.
After an introduction of the technology and a description of current progresses the different
fields of research of imaging mass spectrometry will be presented. In particular its enormous
potential in clinical settings in complement to traditional histopathology and its important role
in the study of drug distribution and effects in various biological tissues will be described.
Finally, a critical outlook will be made towards the developments to be made for the technology
to become a mainstream analytical tool.

SMAP Conference, September 19th-22nd 2011, Avignon


[I7] Ambient Ionization and Miniature Mass Spectrometers
Graham COOKS
Department of Chemistry, Purdue University, West Lafayette IN 47907, US
Contact : cooks@purdue.edu

The recent development of ambient ionization methods is transforming the
applications of mass spectrometry (MS) allowing virtually any sample to be
examined in air, rather than being introduced into the vacuum system. This talk focuses on two
ambient ionization methods: (i) paper spray (PS) in which in which samples are ionized in air,
directly from filter paper (and similar materials including whole plant or animal tissue) and (ii)
desorption electrospray ionization (DESI) in which the sample is impacted by charged
microdroplets which pick up analyte by dissolution and carry it to the MS. The physical basis of
each of these experiments is described.
DESI finds application in disease diagnosis by tissue imaging and examples of human bladder,
liver and brain cancer diagnostics will be given. DESI imaging combines the chemical information
collected for multiple analytes from the mass spectrometer with spatial information, which
makes it useful for analyzing histological sections of biological tissue. Alterations in the
distribution of polar lipids are associated with malignant transformations in tissue. Multivariate
statistical analysis using principal component analysis (PCA) is used to analyze the imaging MS
data, magnifying differences between the lipid profiles of tissue as a function of disease state.
Data showing glioma diagnosis and prostate biomarker recognition will be emphasized.
Whole blood analysis for therapeutic agents is achieved in a few seconds using paper spray.
Remarkably, the method is quantitatively accurate and precise and covers the therapeutic
range for many oncology drugs. The promise of this method for point-of-care diagnostics will
be shown. LTP applications in food safety and bacterial identification also will be described.
Ultimately ambient ionization methods are best used with handheld miniature mass
spectrometers, a combination that has enormous potential to transform in situ chemical
analysis. Progress in interfacing ambient ionization sources to miniature mass spectrometers is
The support of this work by NSF, DOE and the Alfred Mann Foundation at Purdue is gratefully
acknowledged as is ongoing collaboration with Prof. Zheng Ouyang.


SMAP Conference, September 19th-22nd 2011, Avignon

[I8] Proteomics analyzes reveal unexpected aspects of the evolution of phagosomes
over 1.2 billion years
Jonathan Boulais, Matthias Trost, Pierre Thibault, Michel Desjardins
Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal,
Québec, Canada
Contact : michel.desjardins@umontreal.ca

Phagosomes are intracellular organelles formed in a variety of cells following the engulfment of
large particulate materials by phagocytosis. This organelle plays key roles in both innate and
adaptive immunity by promoting the establishment of the molecular properties needed to kill
microorganisms and present some of their antigens on MHC molecules.
In the last 20 years, the striking advances in the field of proteomics and systems biology have
largely contributed to our understanding of the molecular mechanisms regulating phagosome
functions. This presentation will highlight how the application of large-scale approaches has
contributed to reveal novel aspects of the functional properties of phagosomes and their
emergence during evolution.

SMAP Conference, September 19th-22nd 2011, Avignon


[I9] A Novel Strategy in Quantitative Proteomics: Its Implication for Biomedical
Luxembourg Clinical Proteomics Center, CRP-Santé, Strassen, Luxembourg
Contact : bdomon@crp-sante.lu

The generation of accurate and comprehensive data sets has become an essential element of
systems biology and biomarker studies. While large scale discovery experiments one hand and
targeted quantitative analyses on the other are nowadays widely used in proteomics, we are
proposing an alternative approach, which is based on a novel quadrupole/orbitrap instrument.
The high acquisition speed and the exquisite sensitivity of such a hybrid mass spectrometer
allow performing reliable qualitative and quantitative experiments. The additional selectivity
intrinsic to the high resolution orbitrap mass analyzer enables the development of novel
quantification methods. Quantitative experiments can be performed either in full scan mode
(using the high-resolution / accurate mass capability) or in MS/MS mode by analyzing specific
fragment ions (i.e. SRM-like mode). The different modes of operation, their advantages and
limitations will be presented in details. This technique has been applied to precisely quantify
biomarker candidates in bodily fluids, and more specifically in urine samples. The quantitative
analyses were performed in conjunction with stable isotope dilution, using second generation
synthetic polypeptides, composed of one universal reporter fragment facilitating the
systematic, precise quantification of multiple analytes in complex biological samples.


SMAP Conference, September 19th-22nd 2011, Avignon

[I10] A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae
Anne-Claude GAVIN
Structural and Computational Biology Unit, European Molecular Biology Laboratory,
69117 Heidelberg, Germany
Contact : gavin@embl.de

Biological function emerges from the concerted action of numerous
interacting biomolecules. Deciphering the molecular mechanisms behind cellular processes
requires the systematic charting of the multitude of interactions between all cellular
components. While protein–protein and protein– DNA networks have been the subject of many
systematic surveys, others critically important cellular components, such as lipids, have to date
rarely been studied in large-scale interaction screens.
The importance of protein–lipid interactions is evident from the variety of protein domains that
have evolved to bind particular lipids and from the large list of disorders, such as cancer and
bipolar disorder, arising from altered protein–lipid interactions. The importance of lipids in
biological processes and their under-representation in current biological networks suggest the
need for systematic, unbiased biochemical screens. Here, we report a screen to catalog protein–
lipid interactions in yeast using a lipid arrays.
To illustrate the data set’s biological value, we studied further several novel interactions with
sphingolipids, a class of conserved bioactive lipids with an elusive mode of action. Integration of
live-cell imaging suggests new cellular targets for these molecules, including several with
pleckstrin homology (PH) domains. The dataset presented here represents an excellent resource
to enhance the understanding of lipids function in eukaryotic systems.

SMAP Conference, September 19th-22nd 2011, Avignon


[I11] The organization of synapse proteomes
Seth Grant
Wellcome Trust Sanger Institute, Cambridge, Edinburgh University, Edinburgh
Contact : sg3@sanger.ac.uk

Proteomic mass spectrometry has been a groundbreaking technology for
studying the composition of complex subcellular organelles. In the nervous system, proteomics
has discovered more synaptic proteins than any other method and uncovered a remarkable
complexity in the signaling machinery involved in the communication between nerve cells.
These data sets have opened up new insights into the evolution of the brain, the organisation
and architecture of complex circuits and in the diversity of behavior. The presentation will show
how synapse proteomics has introduced molecular complexity into neuroscience and how from
this complexity simple organizational features and novel mechanisms have emerged. Synapse
proteomics has allowed a unique convergence with human genetics leading to the identification
of subsets of proteins that control phenotypes that are involved with many brain diseases. The
study of the human synapse proteome has revealed that postsynaptic proteome is disrupted by
over 200 mutations involved with over 130 brain diseases.


SMAP Conference, September 19th-22nd 2011, Avignon

[I12] Charge Detection Mass Spectrometry
Chemistry Department, Indiana University, Bloomington, Indiana 47401, USA
Contact : mfj@indiana.edu

This presentation will provide an overview of recent work pushing the
boundaries of sensitivity and accuracy with charge detection mass spectrometry. In
conventional mass spectrometry the m/z distribution is obtained for an ensemble of ions, z is
then deduced from the m/z distribution of the ensemble, and the ion mass is obtained from the
corresponding m/z and z. This approach only works when the charge states are resolved in the
m/z distribution, which is usually not the case for large and heterogeneous ions. In charge
detection mass spectrometry, m/z and z are directly measured for each individual ion, so that
the mass can be determined for each ion. This approach allows true mass spectra to be
determined for very large and very heterogeneous ions. The two main challenges with charge
detection mass spectrometry are the sensitivity and accuracy of the charge measurements.
Efforts to attain an accuracy of a single elementary charge (1e) and a sensitivity of 10e will be
described. Applications to ions with masses from kilodaltons to teradaltons will be

SMAP Conference, September 19th-22nd 2011, Avignon


[I13] Mass spectrometry in forensic hair testing : example of drug-facilitated crimes
Pascal KINTZ
X-Pertise Consulting, 84 route de Saverne, 67205 Oberhausbergen, France
Contact : pascal.kintz@wanadoo.fr

The use of a drug to modify a person’s behaviour for criminal gain is not a
recent phenomenon. However, the recent increase in reports of drugfacilitated crimes (sexual assault, robbery) has caused alarm in the general public. Drugs
involved can be pharmaceuticals, such as benzodiazepines (flunitrazepam, lorazepam ...),
hypnotics (zopiclone, zolpidem), sedatives (scopolamine, neuroleptics, some anti-H1) or
anaesthetics (GHB, ketamine), drugs of abuse, such as cannabis, ecstasy or LSD, or more often
To perform successful toxicological examinations, the analyst must follow some important
rules : 1. obtain as soon as possible the corresponding biological specimens (blood, urine and
hair), 2. use sophisticated analytical techniques (LC/MS, HS/GC/MS, tandem mass
spectrometry); and 3. take care on the interpretation of the findings.
Even after the publication of these guidelines for the clinicians, in most cases specimens are
collected at best 24 hours after the crime has occurred.
Drugs used to facilitate sexual assaults can be difficult to detect (active products at low dosages,
chemical instability), possess amnesic properties and can be rapidly cleared from the body
(short half-life). Prohibiting immunoassays and using only hyphenated techniques, substances
can be found in blood for 6 hours to 2 days and in urine for 12 hours to 5 days. In these
situations, blood or even urine can be of poor interest. This is the reason why this laboratory
developed an original approach based on hair testing.
Hair was suggested as a valuable specimen in situations where, as a result of a delay in
reporting the crime, natural processes have eliminated the drug from typical biological
specimens. While there is a lot of papers focused on the identification of drugs in hair following
chronic drug use, those dealing with a single dose are very scarce.
This laboratory recommends to wait for 3-4 weeks after the offense and then collect 4 strands
of about 100 hair. One strand will be used to test for drugs of abuse (mostly for cannabis, but
also for ecstasy related compounds and cocaine that are sometimes observed), one for GHB and
the other one for a screening of 30 various sedatives. The last strand can be used for a potential
counter-analysis. After decontamination, hair is then segmented as follows : 0 to 2 cm (segment
corresponding to the period of crime), 2 to 4 and 4 to 6 cm (which should be drug-free). For
GHB, segments are of 3 mm (n=8).
Conventional GC/MS can be used to test for drugs of abuse, but given the expected
concentrations to measure in low weight segments (in order to avoid the shave the victim), GHB
and sedatives are tested by GC-MS/MS and UPLC-MS/MS, respectively.
The experience of the authors will be documented in cases involving GHB, zolpidem,
bromazepam, alprazolam, scopolamine, alimemazine, diphenhydramine ...
Hair analysis may be a useful adjunct to conventional drug testing in sexual assault. It should not
be considered as an alternative to blood and urine analyses, but as a complement. This
approach may find useful applications, but appears very expensive, given the number of
analyses to achieve with sophisticated equipment.


SMAP Conference, September 19th-22nd 2011, Avignon

[I14] Automated high-throughput analysis of quantitative proteomics data
Applied Bioinformatics, Center for Bioinformatics, Department of Computer Science,
University of Tübingen, Sand 14, 72076 Tübingen, Germany
Contact : oliver.kohlbacher@uni-tuebingen.de

Over the last decade HPLC-MS has become the workhorse in proteomics and
metabolomics. Increasing sensitivity and resolution of the instruments give us unprecedented
coverage of the proteomes and metabolomes under investigation. The flip side of this
development is the amount and complexity of data produced. Similar to what we observe in
next-generation sequencing, bioinformatics analysis of a high-throughput experiment is rapidly
becoming the bottleneck.
In this talk, I will illustrate how wet-lab workflows have to be matched by appropriate data
analysis workflows in order to enable more complex experiments. Based on our software
package OpenMS/TOPP, I will illustrate how analysis workflows can be set up, adapted to
specific experimental designs for different quantification strategies. The resulting analyses can
then be run automatically. Automated workflows also enable more compute-intensive
methods, as computer power scales much better than manual labor done by PhD students and
postdocs. I will give a few examples, how these more complex analyses can result in a drastic
increase in the coverage and accuracy of the experiment.

SMAP Conference, September 19th-22nd 2011, Avignon


[I15] Traveling to the Ends of the Proteome World. Positional N-terminal and Cterminal proteomics deciphers protein terminal and proteolytic posttranslational modifications in the HPP
Christopher OVERALL
UBC Centre for Blood Research, University of British Columbia, 2350 Health Sciences
Mall, Vancouver, B.C. V6T 1Z3 Canada
Contact : chris.overall@ubc.ca
Protein termini are truncated by proteolysis, but the extent to which this molds the proteome in vivo is
unknown. In addition to constitutive proteolysis during protein synthesis and maturation, the processing of a
mature protein often irreversibly changes its activity. Specific degradomics techniques are needed to rapidly
identify and quantify the N- and C-terminomes in order to reveal the extent of post-translational
modifications of protein termini and therefore the functional state of key molecules, the extent of proteolysis
in a system, and to identify new protease substrates. We have devised new approaches to enrich for the N
and C termini of proteins for high throughput terminome analyses of human tissues and cells for the Human
Proteome project, in particular for chromosome 21 that is Canada’s focus for the HPP. Broad coverage Nterminome analysis necessitates a negative selection procedure as the variety of original mature protein Nterminal blocked peptides each present individual chemical hurdles for their enrichment by positive selection
We developed a combined N-terminomics and C-terminomics and protease substrate discovery degradomics
platforms for the simultaneous quantitative analysis of the N-terminome and proteolysis on a proteome-wide
scale called Terminal Amino Isotopic Labelling of Substrates (TAILS, Kleifeld et al Nature Biotech 28, 281-288;
Prudova et al 2010 Mol Cell Proteomics; auf dem Keller et al 2010 Mol Cell Proteomics) and C-TAILS (Schilling
et al Nature Methods 2010). By using novel polymers to deplete the internal tryptic peptides, TAILS suffers
little from sample loss and low yields, so requiring only 100 microgram of sample and one MS/MS analysis per
sample. By a three-day procedure with flexible labelling options, TAILS can be adapted to a variety of
experimental situations including cell culture and complex biological sample analysis. Incorporating iTRAQ
labelling iTRAQ-TAILS also provides wide coverage of all forms of naturally blocked N-terminal peptides and
allows for their quantification through labelling of lysine side-chains in up to 8 samples. In addition to
providing valuable proteome annotation this has several unique advantages. TAILS permits exploitation of the
acetylated and other blocked mature protein N-terminal peptides as a statistical classifier that is then used to
set isotope ratio cut offs that reveal protease activity.
We introduce a novel parameter evaluating ion intensity dependent quantification confidences of single
peptide quantifications. Being a quantitative procedure, TAILS can analyse the substrate degradome of a
broad specificity protease or one with no known specificity without manual data parsing, in the same
experiment, and also do this in vivo. We have applied TAILS to a variety of proteases and compared protease
knock out mice in models of arthritis, skin inflammation and models of breast cancer metastasis and
pancreatic carcinoma in the RIP-Tag model. Typical analyses identify over 3000 N-terminal peptides from
which we found that the removal of the N-terminal methionine is dependent upon the amino acid at position
2 with distinct preferences found for valine, glycine, alanine and serine. In one experiment, acetylation
occurred on 731 original mature protein N-terminal peptides but at the initiator methionine in only 153 of
these instances. In 578 cases, acetylation was at position 2 in the protein after removal of 1Met, with alanine,
serine and methionine being the preferred acetylated residues. Internal acetylation sites exhibit a distinct
acetylation pattern that differs from the N-terminal acetylation. Finally N-terminal positional proteomics
enables MS sample simplification with proteins identified in bronchoalvelar fluid and serum having
abundances spanning a range greater than six orders of magnitude. This underscores the potential of TAILS to
tackle the dynamic range analysis problem in complex proteomes and as a high throughput approach
annotate the N and C termini in the HPP.
Link : http://www.clip.ubc.ca


SMAP Conference, September 19th-22nd 2011, Avignon

[I16] Targeted proteomics from proteins to proteome maps : potential and
Institute of Biochemistry, Department of Biology, ETH Zuerich, Zuerich. Switzerland
Contact : paola.picotti@bc.biol.ethz.ch

Selected Reaction Monitoring (SRM) is a targeted mass spectrometry
technique which emerged in the field of proteomics as a complement to the untargeted
shotgun methods. The main advantages of SRM become apparent when predetermined sets of
proteins need to be measured across multiple samples in a consistent and accurate manner.
The technology is however still in its infancy for protein analysis and several challenges need to
be addressed to demonstrate the power of the technique in biological research and increase its
widespread application in non-specialized laboratories.
To evaluate the applicability of SRM to studying biological networks, we applied it to the
analysis of a metabolic network constituted by proteins covering a broad range of abundances
and including a large number of families of isoenzymes, sharing high sequence overlap. Proteins
in the network were quantified by SRM in yeast cells grown under a series of conditions
inducing radically different metabolic setups and in a growth time-course of cells transiting
through a series of metabolic phases. The quantitative dataset generated highlighted how yeast
metabolism adapts to changing conditions of supply and demand of nutrients and suggested
differential functionality for several isoenzymes. The application showed the potential of the
technique to elucidate the dynamics of cellular networks through large number of perturbing
In order to expand the capabilities of the technique, we used an approach based on libraries of
unpurified synthetic peptides to develop at high-throughput SRM assays for entire proteomes.
We used the method to develop SRM assays for the ~6,000 proteins that constitute the
proteome of S. cerevisiae and then expanded it to the generation of SRM assays for >90% of the
human proteome. The synthetic peptide libraries were also used to generate gold-standard ion
trap spectral libraries to be used for spectral matching of shotgun proteomic datasets in
discovery-driven experiments. The described SRM assays and spectral libraries are currently
being made publicly available via the SRMAtlas user interface, which supports their
dissemination across different laboratoreis. The potential of such proteome maps, for targeted
and discovery proteomics, as well as their limitations will be discussed.

SMAP Conference, September 19th-22nd 2011, Avignon


[I17] Two dimensional FT-ICR, the only way to obtain all the MS/MS correlations
from a sample without selecting the parent ions. Instrumental developments
and analytical applications
Christian ROLANDO
Université Lille 1 Sciences et Technologies, USR CNRS 3290 Miniaturisation pour
l'Analyse, la Synthèse & la Protéomique (MSAP), 59655 Villeneuve d'Ascq Cedex, France
Contact : Christian.Rolando@univ-lille1.fr

The pulse sequence for 2D FT-ICR MS was first developed in 1988 [1] by MS and NMR teams respectively lead
by Tino Gäumann and Geoffrey Bodenhausen [1] based on a key experiment demonstrating cyclotron
excitation reversibility [2] and conveys detailed information for compounds in complex samples in one easily
readable 2D mass spectrum without ion isolation. We revisited 2D FT-ICR MS [3] which, unlike 2D NMR, has
no analytical applications yet. Gas-free fragmentation modes allow us to retain high resolution and sensitivity,
and the advances in electronics and computer technology since 1988 enable broadband acquisition. The
method, however, needs to be optimized in terms of scintillation noise, experiment time and necessary
amounts of sample. In this study, we apply techniques adapted from NMR spectroscopy to optimize 2D FT-ICR
Because in both dimensions the spectrum is obtained after Fourier transforming a signal that has been
sampled at regular time intervals (in the vertical dimension, a delay, and in the horizontal dimension, a
measurement date), the resolution of 2D mass spectra behaves in both dimensions like the resolution in onedimensional FTMS: it increases with the number of data points and is inversely proportional to m/z ratio. In
preliminary experiments, time transients were limited to 32k data points since the 32-bit-written software
cannot handle files larger than 256 Mb. Using 2048 scans leads to hour-long experiments with a resolution of
~1000 in the MS and fragment ion MS/MS dimension but only a few hundred in the correlation parent ion
dimension [3]. For example, we were able to distinguish the fragments of the 79Br and 81Br isotopes and the
C and 13C isotopes of singly charged ions of bromopride, a small brominated drug (molecular weight 344.25
g.mol-1). The new 64-bit version of the NPK package developed by Marc-André Delsuc [4] and NMRTEC allows
us to work on files larger than 16 Gb. An experiment on intact cytochrome C (molecular weight 12 kDalton)
using 8192 scans of 512k points time transients shows line base separation for each multicharged ion bearing
around 10 charges (ca 10 000 resolution) and quadrupole like (1 m/z unit) separation in the correlation
dimension (ca 1000 resolution). Furthermore these experiments show that the resolution in both dimensions
remains inversely proportional to m/z ratio, as expected.
All of our experiments were performed using nanoESI at concentrations of 1 pmol/µL, leading to sample
consumption of less than 20 pmol per hour per experiment, but at the expense of signal intensity fluctuation
which translates into scintillation noise in the 2D data. We adapted the NMR version of the Cadzow denoising algorithm [5] for 2D FT-ICR mass spectra. This algorithm is based on the decomposition of the signal in
singular values from which the signal at longer time may be predicted. The Cadzow noise reduction
dramatically reduced fluctuations and brought out additional fragmentation peaks that were masked by the
noise [6].
Results obtained using IRMPD and ECD fragmentation without any in-cell or quadrupole separation for simple
compounds like individual peptides, the multicharged ion distribution of small proteins and more complex
mixtures like tryptic protein digests will be presented. Finally future development of 2D FT-ICR will be briefly
discussed at the sight of multidimensional NMR methodologies developed during the last twenty years.
[1] P. Pfändler et al., J. Am. Chem. Soc. 110 (1988) 5625-5628
[2] A.G. Marshall et al., Chem. Phys. Letts. 105 (1984) 233-236
[3] M.A. van Agthoven et al., Int. J. Mass Spectrom., doi:10.1016/j.ijms.2010.10.034
[4] D. Tramesel et al., J. Magn. Res. 188 (2007) 56-67
[5] C. Brissac et al., J. Biomol. NMR 6 (1995) 361-365
[6] M.A. van Agthoven et al., Rapid Commun. Mass Spectrom., 25 (2011) 1609–1616.


SMAP Conference, September 19th-22nd 2011, Avignon

[I18] High resolution mass spectrometry at high speed: advances in methods,
techniques and applications
Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de
Lausanne, CH-1015, Lausanne, Switzerland
Contact : yury.tsybin@epfl.ch

High magnetic field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)
provides the unbeatable analytical performance in terms of high resolution measurements.
However, the high resolution measurements require a long experimental time, e.g., 1-20
seconds per single mass spectrum acquisition, and thus are incompatible with the current and
near-future requirements for the high throughput and fast data acquisition, enforced by the
short peptide and protein elution time from the chromatographic column. Here, we will discuss
some of the possible solutions to this problem from both, hardware and signal processing
development. The FT-ICR MS hardware development follows the implementation of ultra-high,
e.g., 21 T, magnetic field environments together with higher acquisition speed and harmonized
ICR ion traps. The recent progress in Orbitrap FTMS development has significantly reduced the
gap between Orbitrap and ICR FTMS in terms of obtained resolving power required for the
mainstream MS applications, 60-200k. Finally, the state-of-the-art time-of-flight (TOF) mass
analyzers have demonstrated a substantial progress in the recent years and now offer 30-60k
resolving powers achieved at comparable times to the high field ICR and Orbitrap FTMS and
faster. On the other hand, incredible progress in the computational power and high frequency
electronics opens the doors to the advanced signal processing development, which received a
particular attention in the recent years. A number of groups, including ours, are in the process
of tailoring the super-resolution signal processing methods, e.g., filter diagonalization method
(FDM), to the needs of the ICR and Orbitrap MS. The goal is to replace the FT-based signal
processing with the methods that would require 10-100 times shorter transient time-domain
signals to yield a similar level of the resolving power.

SMAP Conference, September 19th-22nd 2011, Avignon


[I19] Statistical methods and tools for protein quantification in MS-based
Department of Statistics & Department of Computer Science, Purdue University, West
Lafayette, IN 47907
Contact : ovitek@purdue.edu

The goal of many proteomic experiments is to quantify and compare the abundances of
proteins in complex biological mixtures. This can be accomplished in a variety of mass
spectrometry-based workflows, such as label-free or label-based LC-MS workflows, or label-free
or label-based SRM workflows. Although the experimental details of these workflows vary
greatly, they all output a list of identified and quantified spectral features. There is currently no
consensus on how to appropriately handle the repeated quantitative measurements on a
protein in a sample, and how to derive protein-level conclusions across all labels, features,
samples and conditions.
We propose a general statistical modeling framework for protein quantification based on linear
mixed-effects models. It is applicable to most experimental designs, LC-MS and SRM
experiments, and label-based and label-free SRM workflows. We illustrate the utility of the
framework in a series of investigations with fairly complex designs: a 3-way factorial label-free
LC-MS, and a label-based SRM time course investigation of central carbon metabolism of
S.cerevisiae. We further illustrate the sensitivity and specificity of the framework using
controlled spike-in experiments, and using a series of simulated datasets. Finally, we discuss the
freely available software that we developed to implement the modeling framework.


SMAP Conference, September 19th-22nd 2011, Avignon

Selected short oral communications

SMAP Conference, September 19th-22nd 2011, Avignon


[O1] A
phosphorylation of serotonin 2a receptor upon activation by hallucinogenic
versus non-hallucinogenic agonists
Franck Vandermoere1, Samah Karaki1, Clotilde Mannoury la Cour2, Carine Becamel1, Joel Bockaert1, Mark J
Millan2, Philippe Marin1

Institut de Génomique Fonctionnelle, CNRS UMR5203, 141 rue de la Cardonille, 34094 Montpellier, France


IDR Servier, 125 chemin de Ronde, 78290 Croissy/Seine, Paris, France

Contact: Franck Vandermoere (franck.vandermoere@igf.cnrs.fr)

Keywords: Signaling, interactomics and post-translational modifications
The serotonin 5-HT2A receptor is a primary target of psychedelic hallucinogens such as lysergic
acid diethylamide (LSD), which reproduce some of the core symptoms of schizophrenia. An
incompletely resolved paradox is that only some 5-HT2A receptor agonists exhibit
hallucinogenic activity, whereas structurally related agonists with comparable affinity and
activity do not.
Using quantitative phosphoproteomics combining SILAC, phosphopeptide enrichment by
hydrophilic interaction chromatography /immobilized metal affinity chromatography and FT
mass spectrometry, we compared the phosphoproteome in cells transiently expressing the 5HT2A receptor under three conditions: no-stimulation; exposure to the hallucinogen DOI and
exposure to the non-hallucinogenic agonist lisuride.
Among the 5,996 identified phosphopeptides, 454 sites were differentially phosphorylated upon
exposure to DOI vs. lisuride. These include a serine phosphorylated upon exposure to DOI but
not to lisuride and located in the i3 loop, a region important for 5HT2A desensitization. Mass
spectrometry analysis of immunopurified receptor further confirmed such a differential
phosphorylation. Correspondingly, exposure to hallucinogens induced a less pronounced
receptor desensitization than exposure to non-hallucinogenic agonists.
In conclusion, this phosphoproteomic analysis reveals that 5-HT2A receptor stimulation by
hallucinogenic vs. non hallucinogenic agonists induces contrasting phosphorylation patterns
that may be related to their distinct behavioural responses. It also provides the first
demonstration of differential phosphorylation of a G protein-coupled receptor upon stimulation
by «biased» agonists.
Link: http://www.igf.cnrs.fr/spip.php?article89


SMAP Conference, September 19th-22nd 2011, Avignon

[O2] The Induction of Serine/Threonine Protein Phosphorylations by Native and
Mutant PDGFR/TrkA Chimeras in Stably Transfected PC12 Cells
Jordane Biarc1, Robert Chalkley1, Al Bulingame1, Ralph Bradshaw1

Mass spectrometry facility-UCSF, 600th street, 94158-2517 San Francisco, USA

Contact: Jordane Biarc (jordane.biarc@hotmail.fr)

Keywords: Signaling, interactomics and post-translational modifications
The tyrosine kinase receptor (RTK) TrkA, which is activated by NGF (nerve growth factor)
binding, plays a major role in differentiation and survival of both peripheral and central nervous
system neurons. When PC12 cells, a model paradigm for these functions, are stimulated with
NGF, they extend neurites and acquire characteristics similar to sympathetic neurons. After
stimulation, TrkA undergoes tyrosine autophosphorylation creating docking sites that link
several effectors and adaptors to the activation of downstream signaling pathways, which are
characterized by a second, longer lasting, wave of protein phosphorylation targeted to
serine/threonine residues. The Y490 and Y785 of the receptor play particularly important roles
in these events and stimulate the activation of three main pathways: ERK1/2 via Ras,
phosphatidyl inositol - 3- kinase (PI3K) and PLCγ. However, a much broader array of
phosphorylations is known to occur in both resting and stimulated cells. The aim of this study is
to determine the profile of serine/threonine phosphorylation targets after stimulation of the
TrkA receptor for 20’ and to characterize the precise involvement of Y490 and Y785 in these
To avoid the stimulation of the second receptor of NGF (p75) and endogenous TrkA receptors,
we used chimeric receptors composed of the ectodomain of the platelet-derived growth factor
(PDGF) receptor and the transmembrane and endodomain of the TrkA receptor (denoted PTR),
stably transfected into PC12 cells. The cells, grown in a medium containing heavy/light
lysine/arginine (SILAC), were stimulated for 20 minutes with PDGF and lysed. The tryptic digest
of proteins was enriched for phosphopeptides by a TiO2 column, further fractionated by strong
cation exchange chromatography and analyzed by LC-MS/MS. The analysis of the
phosphoproteome in cells expressing PTR showed quantitative changes in some previously
known entities in signaling pathways, proving the specificity of the method, as well as many
new modified entities. Interestingly, a comparison with a data set from HeLa (human) cells
stimulated for the same time period by EGF (Olsen et al, 2006), showed a similar profile of
protein kinase activation as judged by substrate specificity motifs. Analyses of cells expressing a
PTR Y490F mutant and a PTR Y490/785F double mutant, stimulated under the same conditions,
revealed three major classes of modifications: those dependent on Y490, those dependent on
Y785 and those not dependent on either. This last group could be activated through the
phosphorylation of one or more of the five other endodomain tyrosines of TrkA known to be
phosphorylated but not previously identified as a docking/effector binding site(s). These
activations are presumably not required for neurite proliferation but are likely involved in other
functions stimulated by NGF.
This work was supported by NIH NCRR grant P41 RR001614.

SMAP Conference, September 19th-22nd 2011, Avignon


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