The Proteome: An Overview 

The term “proteome” is derived from “PROTEin component of a genOME,” describing the full complement of proteins present within an organism, tissue, cell, or specific cellular compartment (e.g., mitochondria). Human cells are estimated to contain over two million distinct protein isoforms, called ‘proteoforms’, which drive all cellular metabolic pathways and intracellular signaling networks. 

Proteomics 

Proteomics encompasses the comprehensive analysis of complex protein mixtures, such as cellular lysates or tissue extracts, to reveal both qualitative and quantitative changes across the proteome. Over the past years, due to the constant methodological advancements, this field has become indispensable in the investigation of cellular processes and disease mechanisms. 

Proteomics Services at the CDT-CARD Laboratory 

The Proteomics Laboratory at CDT-CARD offers cutting-edge proteomic services supported by state-of-the-art instrumentation, including the Thermo Scientific Orbitrap Exploris 480 platform for high-resolution mass spectrometry, alongside the Sciex QTRAP 7500 for targeted, high-sensitivity analyses. Core services include: 

Orbitrap Exploris 480 platform 

Comprehensive (proteome-wide) analyses utilizing: 

DDA (data-dependent acquisition), or shotgun proteomics: 

• Label-free methods 

• Isobaric labeling techniques (e.g., TMT, iTRAQ) 

DIA (data-independent acquisition, also termed Next-Generation Proteomics) 

• Label-free methods 

Targeted proteome analyses, employing advanced techniques: 

• PRM (Parallel-Reaction Monitoring) 

• SureQuant
  

Sciex QTRAP 7500 platform 

Highly sensitive targeted analyses include: 

• MRM (Multiple-Reaction Monitoring) 

• MRM3
  

timsUltra AIP platform

Single-Cell Proteomics and Spatial Proteomics

• dda-PASEF
• dia-PASEF
• diagonal-PASEF

Laboratory Infrastructure 

The Proteomics Laboratory at CDT-CARD is equipped with a high-resolution Thermo Scientific Orbitrap Exploris 480 instrument with a FAIMS Pro interface, coupled to an UltiMate 3000 high-performance liquid chromatography (HPLC) system; a high-sensitive Sciex 7500 system coupled to a Waters Acquity UPLC M-Class liquid chromatography platform, and a hybrid timsUltra AIP mass spectrometer equipped with an Evosep Eno chromatographic pump. This configuration enables protein analysis using all modern mass spectrometry–based proteomics techniques, depending on project requirements, with next-generation proteomics (NGP) based on data-independent acquisition (DIA) as the primary analytical platform. Additional capabilities include advanced analytical methodologies such as MRM3 and SureQuant. The high resolution of the Exploris 480 instrument (up to 480,000) allows full exploitation of quantitative approaches based on isobaric labeling strategies (e.g., TMT, iTRAQ). The high sensitivity of the timsUltra AIP instrument enables single-cell proteomics (SCP) and spatial proteomics (SP) analyses. For these applications, a cellenONE workstation is employed, allowing sample preparation from limited amounts of biological material.

Applications in Molecular Medicine 

Proteomics bridges gene expression data with the functional context of expressed proteins. Thus it plays a critical role in modern molecular medicine applications, from drug discovery and development to innovative diagnostic strategies. Identifying disease-specific protein expression changes or discovering novel biomarkers represents one of the most challenging yet promising objectives in clinical proteomics, supporting the progression of personalized therapeutic approaches i.a. for civilization diseases. 

photo on main page of laboratories – OPI PIB