National Research Council of Italy

Institute of Biosciences and BioResources

DISBA logo CNR logo

Mass Spectrometry and Proteomics Lab - Naples

Dionex BioLC system

Dionex BioLC system


The Mass Spectrometry and Proteomics laboratory at IBBR-Naples was set up in 2006 by financial investments of University consortium BioTecNet and CNR in order to meet the necessity to establish proteomics-based research at the institute. The goals of facility are three-fold:

  • provide analytical measurements and supports to studies and projects requiring proteomics technology, data analysis and/or mass spectrometry-based analysis;
  • develop new methodologies and analytical tools for functional proteomics;
  • facilitate the acquisition of external research funds to promote interdisciplinary research and education.

LC Packings Ultimate 3000 2D-nano-HPLC

LC Packings Ultimate 3000 2D-nano-HPLC

Available instruments

  • QSTAR® Elite (Applied Biosystems): a hybrid quadrupole-time-of-flight (Q-TOF) tandem mass spectrometer (MS/MS). The instrument is equipped with a nano-electrospray ion source and on-line coupled to a two-dimensional (2D) nano-HPLC system (Ultimate 3000). The nano-2D-HPLC-ESI-MS system is equipped with an autosampler.
  • HPLC systems
    • Ultimate 3000 (LC Packings) 2D-nano-HPLC interfaced with QSTAR-Elite
      Hewlett Packard, Series 1100 HPLC with UV detector
    • Perkin-Elmer, Series 200 with autosampler
    • Dionex BioLC® system: high performance anion exchange HPAE chromatography with pulsed amperometry detection (PAD) for carbohydrate analysis.
  • ETTAN-DALT II (Amersham): 2D gel electrophoresis system
  • Novex® NuPAGE® SDS-PAGE gel and Novex® NativePAGE™ gel systems
  • nano-ESI ion source

    nano-ESI ion source

    iBlot® Dry Blot and iBind™ Western Blot systems

The Mass Spectrometry and Proteomics Lab provides the following:

Sample preparation

  • Determination of protein concentration (micro BCA assay by NanoDrop analysis and Bradford assay)
  • Desalification and purification of peptide or protein sample for MS scale analysis (like ZipTip)
  • Depletion of high abundant proteins in biological fluids
  • In-solution enzymatic protein digestion
  • In-gel protein digestion
  • PE Series 200 with autosampler

    PE Series 200 with autosampler

    Protein extraction from cell culture and biological fluids
  • Stable isotope labelling for quantitative proteomics using iTRAQ and SILAC
  • Enrichment in phosphopeptides using TiO2 or ZrO2 micro and nano-particles
  • Chromatographic- and gel-based purification and/or separation of proteins

Mass Spectrometry and Related Services

  • In-gel and/or in-solution digestion-based identification of proteins - shotgun analysis
  • Multidimensional protein identification technology (MuDPIT) by nano-HPLC-ESI-MS/MS
  • Set-up of Information Dependent Acquisition (IDA) for the analysis of peptides
  • 2D-nano-HPLC-ESI-MS/MS analysis (1st dimension by SCX and 2nd dimension by C18
  • Gel-besed separation techniques

    Gel-besed separation techniques

    Phosphoproteomics: identification and quantitation of protein phosphorylation by phosphopeptide enrichment and shotgun proteomics
  • Quantitative proteomics by iTRAQ and SILAC technologies
  • ESI-MS or nano-ESI-MS by sample infusion
  • ESI-MS/MS or nano-ESI-MS/MS by sample infusion
  • HPLC-ESI-MS of intact proteins (RP-C4)
  • Exact molecular mass determination - elemental composition (with expected error in 5ppm)

Data analysis

  • Protein identification by automated database search (Mascot Server)
  • QSTAR-Elite-nano-ESI-MSMS


    Manual - Partial sequencing of peptides
  • Elaboration of quantitative proteomics data

The access to the lab is easy and friendly: researchers contact lab staff, discuss experiment, fill up the sample analysis request form, submit the samples and in a few days have their results.


Dr. Gabriella Pocsfalvi and Immacolata Fiume

(click on name to browse their personal pages)

Istituto di Bioscienze e Biorisorse (IBBR/CNR)
Via G. Amendola 165/A, I-70126 Bari (Italy)
Copyright © 2012-2024. All Rights Reserved.