Chapter 7
SWATH-MS Protocols in Human Diseases
Maria del Pilar Chantada-Va ´ zquez, Marı ´a Garcı ´a Vence, Antonio Serna,
Cristina Nu ´ n ˜ ez, and Susana B. Bravo
Abstract
Identification of molecular biomarkers for human diseases is one of the most important disciplines in
translational science as it helps to elucidate their origin and early progression. Thus, it is a key factor in
better diagnosis, prognosis, and treatment. Proteomics can help to solve the problem of sample complexity
when the most common primary sample specimens were analyzed: organic fluids of easy access. The latest
developments in high-throughput and label-free quantitative proteomics (SWATH-MS), together with
more advanced liquid chromatography, have enabled the analysis of large sample sets with the sensitivity and
depth needed to succeed in this task. In this chapter, we show different sample processing methods (major
protein depletion, digestion, etc.) and a micro LC-SWATH-MS protocol to identify/quantify several
proteins in different types of samples (serum/plasma, saliva, urine, tears).
Key words Biological fluids, SWATH-MS, Label-free quantification, Serum/plasma, Saliva, Urine,
Tears, Nanoproteomics
1 Introduction
Proteins are the principal effectors on the major part of the
biological process, and the deregulation of their functions can be
the most important key in the disease process. Therefore, the search
for these deregulated proteins is one of the most crucial issues in
translational science. It is important not only in the search of the
knowledge of the pathology process but also in the pursuit of some
proteins (biomarker) that give us the important information over
the early stage or progression of the disease [1, 2]. These proteins
can be deregulated in their expression levels or their posttranscriptional modifications (PTMs) [3]. The FDA (Food and Drug
Administration) defined a biomarker as a quantifiable biological
parameter that is measured and evaluated as an indicator of normal
biological, pathogenic, or pharmacologic responses to a therapeutic
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_7, © Springer Science+Business Media, LLC, part of Springer Nature 2021
Maria del Pilar Chantada-Va ´zquez and Marı ´a Garcı ´a Vence contributed equally with all other contributors.
105
SWATH-MS Protocols in Human Diseases
Maria del Pilar Chantada-Va ´ zquez, Marı ´a Garcı ´a Vence, Antonio Serna,
Cristina Nu ´ n ˜ ez, and Susana B. Bravo
Abstract
Identification of molecular biomarkers for human diseases is one of the most important disciplines in
translational science as it helps to elucidate their origin and early progression. Thus, it is a key factor in
better diagnosis, prognosis, and treatment. Proteomics can help to solve the problem of sample complexity
when the most common primary sample specimens were analyzed: organic fluids of easy access. The latest
developments in high-throughput and label-free quantitative proteomics (SWATH-MS), together with
more advanced liquid chromatography, have enabled the analysis of large sample sets with the sensitivity and
depth needed to succeed in this task. In this chapter, we show different sample processing methods (major
protein depletion, digestion, etc.) and a micro LC-SWATH-MS protocol to identify/quantify several
proteins in different types of samples (serum/plasma, saliva, urine, tears).
Key words Biological fluids, SWATH-MS, Label-free quantification, Serum/plasma, Saliva, Urine,
Tears, Nanoproteomics
1 Introduction
Proteins are the principal effectors on the major part of the
biological process, and the deregulation of their functions can be
the most important key in the disease process. Therefore, the search
for these deregulated proteins is one of the most crucial issues in
translational science. It is important not only in the search of the
knowledge of the pathology process but also in the pursuit of some
proteins (biomarker) that give us the important information over
the early stage or progression of the disease [1, 2]. These proteins
can be deregulated in their expression levels or their posttranscriptional modifications (PTMs) [3]. The FDA (Food and Drug
Administration) defined a biomarker as a quantifiable biological
parameter that is measured and evaluated as an indicator of normal
biological, pathogenic, or pharmacologic responses to a therapeutic
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_7, © Springer Science+Business Media, LLC, part of Springer Nature 2021
Maria del Pilar Chantada-Va ´zquez and Marı ´a Garcı ´a Vence contributed equally with all other contributors.
105