Mass Spectrometry Core Facility

Marta Vilaseca

Core Facility Manager

Office Tel : +34 93 40 39815

e-mail : marta.vilasecairbbarcelona.org

Background

Set up in September 2007, the Mass Spectrometry Core Facility provides the research community at IRB Barcelona and researchers from external institutions with modern chromatographic and mass spectrometric tools for the identification and characterisation of a broad range of biological species.

The facility is equipped with high accuracy and high resolution mass spectrometers with newly incorporated mass spectrometry (MS) techniques such as ion mobility spectrometry (IM) coupled to high performance tandem MS, Fourier-transform ion cyclotron resonance MS with ECD (electron capture dissociation) and IRMPD (infrared multiphoton dissociation) fragmentation techniques.

The facility performs method development for the identification and characterisation of various biological species, from small molecules to large biomolecules (e.g. intact proteins). Non-covalent protein-protein and protein-ligand interactions are also studied by MS and IM/MS to gain insight into the mechanisms of action of these proteins in biological processes.

Protein identification and quantitation by classical proteomic approaches are performed in collaboration with the PCB’s Proteomics Platform.

The facility also provides consultancy services and analytical method development for specific applications, as well as mass spectra data processing. Samples are analysed either directly by the service or by researchers (previously trained by Facility members), who can use mass spectrometers through an open-access system.

For more information, please contact the facility manager at marta.vilasecairbbarcelona.org

More info

• Mass Spectrometry Request Form
• 2009 Scientific Report - Mass Spectrometry Core Facility
• 2008 Scientific Report - Mass Spectrometry Core Facility
• 2007 Scientific Report - Mass Spectrometry Core Facility

Mass Spectrometry Core Facility

The services offered include MS, MS/MS and MSn analysis using atmospheric pressure ionisation techniques (electrospray and APcI) coupled to LC, nanoLC or infusion inlets.

Lines of expertise:

• Intact protein analysis. Top-down. Middle-down
• MS and IM-MS analysis of non-covalent complexes
• Peptide enzymatic digests analysis (MS, MS/MS) for protein identification and post-translational modifications (PTMs) determination. Bottom-up MS-based proteomics (in coordination with the PCB's Proteomic Platform)
• Small molecule analysis for exact mass determination

The facility provides consultancy services and analytical method development for specific applications, as well as mass spectra data processing. Samples are analysed either directly by the service or by researchers (previously trained by facility members), who can use mass spectrometers through an open-access system.

Equipment and specialised applications:

1-LTQ FT Ultra (Thermo Scientific). Hybrid Mass Spectrometer consisting of a linear Ion Trap, combined with a Fourier Transform Ion Cyclotron Cell. It is also provided with ECD and IRMPD for complementary protein fragmentation in the mass spectrometer. This instrument is used to perform Top-down MS protein analysis and Bottom-up applications. In its normal configuration, this instrument works coupled to an LC device (Surveyor LC (Thermo) and a chip-based nanoESI interface (Advion Triversa Nanomate).

2-Synapt High Definition MS System (Waters-Micromass). Hybrid QTOF instrument with an incorporated Triwave Cell. This instrument allows tandem MS to be combined with ion mobility, thus permitting the analysis of samples differentiated not only by their mass to charge ratio, but also by their shape and size. The instrument is used to analyse the macromolecular structure and conformation of intact proteins and to study non-covalent interactions. When working in its normal configuration, it is attached to a chip-based nanoESI interface (Advion Triversa Nanomate), thus combining the analysis of samples by infusion mode and by nanoLC coupling (NanoAcquity UPLC, Waters; purchased in 2009).

3-LCT-Premier XE (Waters-Micromass). Orthogonal acceleration time-of-fight mass spectrometer ideal for the analysis of high molecular weight compounds. This instrument has been modified to achieve inert conditions inside the ionisation source, in order to allow amide H/D exchange experiments for the study of the dynamic and structural properties of proteins and their complexes. In another set-up configuration, it is used to analyse small molecules for their structural characterisation and provides accuracies of less than 3ppm. For LC-purifications, it is normally attached to an LC device (UPLC Acquity, Waters).

Mass Spectrometry Core Facility

Before sample submission:

Contact the MS team. We advise you on the best analytical methodology for your specific application.

Sample submission/reception:

There are two ways to submit samples for MS analysis:

1. Submission to the technician-run service by filling in the sample/s request form (available here or in the MSC lab).
2. Self-service (open-access) systems. Only for researchers qualified and trained to operate the mass spectrometers.
   If you plan to use the MS service often and would like to be considered for training, please contact Dr. Marta Vilaseca.

Custody and maintenance of samples:

When filling the request form, your sample or set of samples will be identified by a code number (apart from the users label). Depending on the analysis requested it will be classified in the corresponding "to-run" folder for each instrument.

The sample will be also classified and kept in the conditions specified in the request form.

If preferred you can keep your sample and bring it a day before the beginning of analysis (following scheduled dates).

Time of response for an analysis:

There is a calendar (contact the facility manager) for each instrument and submissions will be ordered by time of entry (IRB Barcelona groups are given preferential treatment).

Given the diversity of applications, some of which require only fast analysis while others require longer analysis time, the calendar will be organised as follows:

• Users can reserve a week in a specific instrument for long application (maximum 2 full weeks per user, depending on demand).
• Between long time applications we always reserve a week to perform shorter analysis in order to avoid delays.
• Mondays (or a pre-specified day) are reserved for the maintenance of the equipment and set up of the required technique pretended to use that week in each instrument.

Results delivery

Results performed by MS staff will be given in printed format (spectra and report specifying analytical conditions). Digital format data can also be kept if requested.

If further processing of your results is required a computer will be reserved in the facility for this purpose.

Our future goal is that users can also access data via a secured network. Data will be transferred to a common-server and back-ups will be performed automatically by the ITS Department. Data will be kept for a maximum of two years.

Mass Spectrometry Core Facility

© Photos by Gianluca Battista/Massimiliano Minocri

Core Facility Manager
Marta Vilaseca
tel +34 93 40 39815
e-mail: marta.vilasecairbbarcelona.org

Senior Research Officer
Marina Gay
tel +34 93 40 39815
e-mail: marina.gayirbbarcelona.org

Research Officers
Mª Del Mar Vilanova
tel +34 93 40 39815
e-mail: mar.vilanovairbbarcelona.org

Mass Spectrometry Core Facility

ABeta40 and ABeta42 amyliod fibrils exhibit distinct molecular recycling properties
Sánchez L, Madurga S, Pukala T, Vilaseca M, López-Iglesias C, Robinson CV, Giralt E, Carulla
J Am Chem Soc, 133 (17), 6505-6508 (2011)

On the role of flexibility in protein-ligand interactions: the example of p53 tetramerization domain
Gordo S, Martos V, Menendez M, Vilaseca M, Mendoza J, Giralt E
Chem As J, 6 (6), 1463-1469 (2011)

Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns
Borg J, Campos A, Diema C, Omeñaca N, de Oliveira E, Guinovart J, Vilaseca MJ
Clin Proteom, 8 (6) (2011)

Enhanced reactivity of Lys182 explains the limited efficacy of biogenic amines in preventing the inactivation of Glucose-6-Phosphate Dehydrogenase by Methylglyoxal
Flores-Morales P, Diema C, Vilaseca M, Estelrich J, Luque FJ, Gutiérrez-Oliva S, Toro-Labbé A, Silva E.
Biorg Med Chem, 19, 1613-1622 (2011)

Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post-translational modifications
Casado-Vela J, Cebrián A, del Pulgar MT, Sánchez-López E, Vilaseca M, Menchén L, Diema C, Sellés-Marchart S, Martínez-Esteso MJ, Yubero N, Bru-Martínez R, Lacal JC
Proteomics, 11, 590-603 (2011)

New insights into the factors that govern the square/triangle equilibria of Pd(II) and Pt(II) supramolecules. Unexpected participation of a mononuclear species in the equilibrium
Ferrer M, Pedrosa A, Rodríguez L, Rossell O, Vilaseca M.
Inorganic Chemistry, 49, 9438-9449 (2010)

Molecular recognition at protein surface in solution and gas phase: Five VEGF peptidic ligands show inverse affinity when studied by NMR and CID-MS.
Dyachenko A, Goldflam M, Vilaseca M, Giralt E.
Biopolymers, 6 (94), 689-700 (2010)

Does the solid-phase synthesis of a tetrapeptide represent a challenge at the onset of the XXI century? The case of cyclo[(3R)-3-hydroxydecanoyl-L-seryl-(3R)-3-hydroxydecanoyl-L-seryl]
Teixidó M, Caba JM, Prades R, Zurita E, Martinell M, Vilaseca M, Albericio F and Giralt E.
Int J Peptide Res Therapeutics, 13, 313-327 (2007)

Solid-state aggregates with unconventional (C-H)+...Cl- hydrogen bonding revealed by X-ray diffraction
Alcalde E, Mesquida N, Vilaseca M, Alvarez-Rúa C and García-Granda S.
Imidazolium-based dicationic cyclophanes. J Supramol Chem, 19 (7), 501-509 (2007)

Imidazolium-based dicationic cyclophanes. Solid-state aggregates with unconventional (C-H)+...Cl- hydrogen bonding revealed by X-ray diffraction
Alcalde E, Mesquida N, Vilaseca M, Alvarez-Rúa C, García-Granda S.
Supramolecular Chemistry, 7 (19), 501-509 (2007)

Proteomic analysis of prodigiosin-induced apoptosis in a breast cancer mitoxantrone resistant (MCF-7 MR) cell line
Monge M, Vilaseca M, Soto-Cerrato V, Montaner B, Giralt E, Pérez-Tomás R.
Invest New Drugs, 25, 21-29 (2007)

A straightforward synthesis of 5'-peptide oligonucleotide conjugates using N(alpha)-Fmoc-protected amino acids
Ocampo SM, Albericio F, Fernández I, Vilaseca M, Eritja R.
Organic Letters, 7 (20), 4349-4352 (2005)

Cell cycle arrest and proapoptotic effects of the anticancer cyclodepsipeptide serratamolide (AT514) are independent of p53 status in breast cancer cells
Soto-Cerrato V, Montaner B, Martinell M, Vilaseca M, Giralt E, Pérez-Tomás R.
Biochemical Pharmacology, 71, 32-41 (2005)