Chapter 13
Shotgun Proteomics for Food Microorganism Detection
Ana G. Abril, Ignacio Ortea, Jorge Barros-Vela ´ zquez,
Toma ´ s G. Villa, and Pilar Calo-Mata
Abstract
Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography–electrospray ionizationtandem mass spectrometry (LC–ESI-MS/MS) has been used for the analysis of bacterial pathogen strainspecific diagnostic peptides allowing the characterization of bacterial strains.
Here, we describe the analysis of tryptic digestion peptides by LC–ESI-MS/MS to search for specific
biomarkers useful for the rapid identification of, on the one hand, the bacterial species and, on the other
hand, the physiological and biochemical characteristics such as the expression of virulence factors, including
toxins, immune-modulatory factors, and exoenzymes.
Key words Microorganism detection, LC–ESI-MS/MS, Mass spectrometry, Peptide biomarker
1 Introduction
The official methods used at clinical laboratories for the identification and characterization of pathogens are the classical and culturebased methods [1, 2]. These methods are slow and labor-intensive,
in contrast to molecular microbial diagnostic methods based on
genomics and proteomics, which allow for a faster and more effective species detection and identification, strain biotyping [3–7], and
even the characterization of bacterial strains with the description of
physiological and biochemical characteristics such as the expression
of virulence factors and related aspects.
Actually, molecular methods for the detection of bacteria in
foods are based on the specific detection of genes by PCR; however,
in certain cases, the difficulty is the availability of universal primers.
This happens, for example, for the detection of biogenic amineproducing bacteria in foods before the biogenic amine is
produced [8].
On the other hand, the proteomic techniques focused on mass
spectrometry are the recent methods that are quickly developing,
Mo ´ nica Carrera and Jesu ´ s Mateos (eds.), Shotgun Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2259,
https://doi.org/10.1007/978-1-0716-1178-4_13, © Springer Science+Business Media, LLC, part of Springer Nature 2021
205
Shotgun Proteomics for Food Microorganism Detection
Ana G. Abril, Ignacio Ortea, Jorge Barros-Vela ´ zquez,
Toma ´ s G. Villa, and Pilar Calo-Mata
Abstract
Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography–electrospray ionizationtandem mass spectrometry (LC–ESI-MS/MS) has been used for the analysis of bacterial pathogen strainspecific diagnostic peptides allowing the characterization of bacterial strains.
Here, we describe the analysis of tryptic digestion peptides by LC–ESI-MS/MS to search for specific
biomarkers useful for the rapid identification of, on the one hand, the bacterial species and, on the other
hand, the physiological and biochemical characteristics such as the expression of virulence factors, including
toxins, immune-modulatory factors, and exoenzymes.
Key words Microorganism detection, LC–ESI-MS/MS, Mass spectrometry, Peptide biomarker
1 Introduction
The official methods used at clinical laboratories for the identification and characterization of pathogens are the classical and culturebased methods [1, 2]. These methods are slow and labor-intensive,
in contrast to molecular microbial diagnostic methods based on
genomics and proteomics, which allow for a faster and more effective species detection and identification, strain biotyping [3–7], and
even the characterization of bacterial strains with the description of
physiological and biochemical characteristics such as the expression
of virulence factors and related aspects.
Actually, molecular methods for the detection of bacteria in
foods are based on the specific detection of genes by PCR; however,
in certain cases, the difficulty is the availability of universal primers.
This happens, for example, for the detection of biogenic amineproducing bacteria in foods before the biogenic amine is
produced [8].
On the other hand, the proteomic techniques focused on mass
spectrometry are the recent methods that are quickly developing,
Mo ´ nica Carrera and Jesu ´ s Mateos (eds.), Shotgun Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2259,
https://doi.org/10.1007/978-1-0716-1178-4_13, © Springer Science+Business Media, LLC, part of Springer Nature 2021
205