Proteomic Analysis of Tears and Conjunctival Cells Collected with Schirmer Strips Using timsTOF Pro: Preanalytical Considerations

This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts—the bulb (B) and the rest of the strip (R)—with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were...

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Published inMetabolites Vol. 12; no. 1; p. 2
Main Authors Akkurt Arslan, Murat, Kolman, Ioannis, Pionneau, Cédric, Chardonnet, Solenne, Magny, Romain, Baudouin, Christophe, Brignole-Baudouin, Françoise, Kessal, Karima
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 21.12.2021
MDPI
Subjects
Biochemistry, Molecular Biology
Biomarkers
Cellulose acetate
Chromatography
Conjunctiva
Data acquisition
Datasets
Enzymes
Genomics
Human health and pathology
Life Sciences
Mass spectroscopy
Mobility
Peptides
Proteins
proteome
Proteomes
Proteomics
Schirmer strip
Scientific imaging
Sensory Organs
signaling pathways
tears
timsTOF Pro
timsTOF Pro
signaling pathways
tears
Schirmer strip
proteome
Online AccessGet full text
ISSN2218-1989
2218-1989
DOI10.3390/metabo12010002

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Abstract This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts—the bulb (B) and the rest of the strip (R)—with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were collected from two healthy subjects at four different visits to be separated into three batches, i.e., 4W, 4B, and 4R. In total, 1582 proteins were identified in the W, B, and R batches. Among all identified proteins, binding proteins (43.4%) and those with catalytic activity (42.2%) constituted more than 80% of the molecular functions. The most represented biological processes were cellular processes (31.2%), metabolic processes (20.8%), and biological regulation (13.1%). Enzymes were the most represented protein class (41%), consisting mainly of hydrolases (47.5%), oxidoreductases (22.1%), and transferases (16.7%). The bulb (B), which is in contact with the conjunctiva, might collect both tear and cell proteins and therefore promote the identification of more proteins. Processing B and R separately before mass spectrometry (MS) analysis, combined with the high data acquisition speed and the addition of ion-mobility-based separation in the timsTOF Pro, can bring a new dimension to biomarker investigations of a limited sample such as tear fluid.
AbstractList This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts—the bulb (B) and the rest of the strip (R)—with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were collected from two healthy subjects at four different visits to be separated into three batches, i.e., 4W, 4B, and 4R. In total, 1582 proteins were identified in the W, B, and R batches. Among all identified proteins, binding proteins (43.4%) and those with catalytic activity (42.2%) constituted more than 80% of the molecular functions. The most represented biological processes were cellular processes (31.2%), metabolic processes (20.8%), and biological regulation (13.1%). Enzymes were the most represented protein class (41%), consisting mainly of hydrolases (47.5%), oxidoreductases (22.1%), and transferases (16.7%). The bulb (B), which is in contact with the conjunctiva, might collect both tear and cell proteins and therefore promote the identification of more proteins. Processing B and R separately before mass spectrometry (MS) analysis, combined with the high data acquisition speed and the addition of ion-mobility-based separation in the timsTOF Pro, can bring a new dimension to biomarker investigations of a limited sample such as tear fluid.
This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts-the bulb (B) and the rest of the strip (R)-with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were collected from two healthy subjects at four different visits to be separated into three batches, i.e., 4W, 4B, and 4R. In total, 1582 proteins were identified in the W, B, and R batches. Among all identified proteins, binding proteins (43.4%) and those with catalytic activity (42.2%) constituted more than 80% of the molecular functions. The most represented biological processes were cellular processes (31.2%), metabolic processes (20.8%), and biological regulation (13.1%). Enzymes were the most represented protein class (41%), consisting mainly of hydrolases (47.5%), oxidoreductases (22.1%), and transferases (16.7%). The bulb (B), which is in contact with the conjunctiva, might collect both tear and cell proteins and therefore promote the identification of more proteins. Processing B and R separately before mass spectrometry (MS) analysis, combined with the high data acquisition speed and the addition of ion-mobility-based separation in the timsTOF Pro, can bring a new dimension to biomarker investigations of a limited sample such as tear fluid.This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts-the bulb (B) and the rest of the strip (R)-with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were collected from two healthy subjects at four different visits to be separated into three batches, i.e., 4W, 4B, and 4R. In total, 1582 proteins were identified in the W, B, and R batches. Among all identified proteins, binding proteins (43.4%) and those with catalytic activity (42.2%) constituted more than 80% of the molecular functions. The most represented biological processes were cellular processes (31.2%), metabolic processes (20.8%), and biological regulation (13.1%). Enzymes were the most represented protein class (41%), consisting mainly of hydrolases (47.5%), oxidoreductases (22.1%), and transferases (16.7%). The bulb (B), which is in contact with the conjunctiva, might collect both tear and cell proteins and therefore promote the identification of more proteins. Processing B and R separately before mass spectrometry (MS) analysis, combined with the high data acquisition speed and the addition of ion-mobility-based separation in the timsTOF Pro, can bring a new dimension to biomarker investigations of a limited sample such as tear fluid.
Author Kessal, Karima
Pionneau, Cédric
Magny, Romain
Brignole-Baudouin, Françoise
Akkurt Arslan, Murat
Chardonnet, Solenne
Kolman, Ioannis
Baudouin, Christophe
AuthorAffiliation 5 Ambroise Paré, Assistance Publique-Hôpitaux de Paris APHP, Service d’Ophtalmologie, Université Paris Saclay, 92100 Boulogne, France
4 Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Service 3, 75012 Paris, France
2 Institut National de la Santé et de la Recherche Médicale INSERM, UMS PASS, Plateforme Post-Génomique de la Pitié Salpêtrière (P3S), Sorbonne Université, 75013 Paris, France; cedric.pionneau@sorbonne-universite.fr (C.P.); solenne.chardonnet@sorbonne-universite.fr (S.C.)
6 Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Laboratoire d’Ophtalmobiologie, 75012 Paris, France
3 Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DGOS CIC 1423, IHU ForeSight, 75012 Paris, France
7 Faculté de Pharmacie, Université de Paris, 75006 Paris, France
1 Institut National de la Santé et de la Recherche Médicale INSERM UMR 968, CNRS UMR 7210, Institut de la Vision, IHU ForeSight, Sorbonne Université UM80, 75012 Paris, France; murat.akkurt@inserm.fr
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– name: 6 Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Laboratoire d’Ophtalmobiologie, 75012 Paris, France
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Issue 1
Keywords timsTOF Pro
signaling pathways
tears
Schirmer strip
proteome
Language English
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Snippet This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts—the bulb (B) and the...
This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts-the bulb (B) and the...
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StartPage 2
SubjectTerms Biochemistry, Molecular Biology
Biomarkers
Cellulose acetate
Chromatography
Conjunctiva
Data acquisition
Datasets
Enzymes
Genomics
Human health and pathology
Life Sciences
Mass spectroscopy
Mobility
Peptides
Proteins
proteome
Proteomes
Proteomics
Schirmer strip
Scientific imaging
Sensory Organs
signaling pathways
tears
timsTOF Pro
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Title Proteomic Analysis of Tears and Conjunctival Cells Collected with Schirmer Strips Using timsTOF Pro: Preanalytical Considerations
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