Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research

Abstract

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein-protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide "molecular pictures", which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.

Keywords: MALDI; biomarkers; biomedical research; proteomics; tandem mass spectrometry (MS/MS).

Figure 1

General representation of the desorption/ionization principle in MALDI-MS. Using a UV laser pulse, a matrix/analyte-particle cloud is desorbed from the co-crystalline matrix/sample solid solution deposited on a metal target. Proton-transfer from matrix ions is thought to be primarily responsible for the subsequent generation of analyte ions that are transferred to the mass analyzer and detected.

Figure 2

MALDI ToF mass spectra in reflectron (A) and linear (B) of intact ECP peptide with DHB as matrix.

Figure 3

MALDI ToF mass spectra in reflectron (A) and linear (B) of intact ECP nitrated peptide with DHB as matrix where the NO₂ group of nitro tyrosine is photcehmical degraded due to UV laser radiation in MALDI ionization source.

Figure 4

MALDI-MSI molecular pictures obtained by MALDI tandem mass spectrometry imaging for in situ identification of proteins: (a) Human visual cortex, myelin basic protein (red), neuromodulin (green), and hemoglobinβ (blue), MALDI-LTQ-Orbitrap instrument [75]; (b) rat small intestine, endogenous protein biomarkers in lamina propria (green), epithelium (blue), and submucosal layer (red), MALDI-ToF/ToF instrument [78]; (c) mouse model glioblastoma 60S ribosomal protein L34, MALDI-ToF/ToF instruments [83]; (d) AD hippocampal section, MUC19 isoform 5 (green), MALDI-ToF/TOF instrument [76]; (e) mouse pituitary gland, anterior lobe (green), vasopressin (red), γ-MSH (blue), MALDI-LTQ-Orbitrap [82]; (f) human articular cartilage, fibronectin distribution [77]; (g) Libechov minipig skin, normal skin, MALDI-ToF/ToF [81]. Reprinted and adapted with permission from Neagu A.-N., 2019. Proteome Imaging: [28].

Figure 5

In-tissue proteomics workflow based on direct and tandem MALDI-MSI.

Figure 6

MALDI MS/MS proteomics workflow for tissue homogenates/cell lysates and biofluid analysis.