Table 2.
List of proteomics studies used for analytical description of the tear film.
| Tear sampling method | Authors, year of publication | Number of healthy subjects, samples, extraction method (only for ScS) | Peptide fractionation | Mass spectrometry technology | Protein identification criteria | Number of proteins identified |
|---|---|---|---|---|---|---|
| Capillary tube | De Souza et al., Genome Biol., 200629 | Pooled samples (from one subject) | pre-fractionation of proteins with 1D SDS-PAGE (13 fractions) or in-solution digestion of whole samples (without fractionation) | LTQ-FT and LTQ-Orbitrap |
Two peptides with Mascot scores of > 35, Two peptides with Mascot scores of > 27 (p ≤ 0.01), or one peptide with a Mascot score of > 54 (p ≤ 0.0001), when MS3 was performed |
491 |
| Kandhavelu et al., J. Proteomics, 201631 | Pooled samples (from 9 subjects) | 1D SDS-PAGE pre-fractionation of proteins (26 fractions) or N-linked glycoprotein enrichment | LTQ-Orbitrap Velos Pro | One unique peptide, FDR < 5% | 1873 | |
| Hua et al., BMC Ophthalmol., 202032 | 3 samples (from 3 subjects) | In-solution digestion of whole samples (no pre-fractionation) | LTQ-Orbitrap XL | FDR < 1% | 949 | |
| Nättinen et al., Trans. Vis. Sci. Tech., 202030 | 31 samples (from 31 subjects) | In-solution digestion of whole samples (no pre-fractionation) |
TripleTOF 5600 + in SWATH-MS mode |
FDR < 1% | 404 | |
| Ponzini et al., Int. J. Mol. Sci., 202133 | 23 samples (from 23 subjects) | In-solution digestion of whole samples (no pre-fractionation) | Orbitrap fusion | One unique peptide, FDR of < 1% | 932 | |
| Schirmer strip | Zhou et al., J. Proteomics, 201224 | 4 ScS (from 4 subjects), samples extracted in 100 mM AmBic, at room temperature for 3 h |
Offline SCX fractionation of peptides (6 fractions) |
TripleTOF 5600 | FDR < 1% for peptides | 1543 |
| Aass et al., Anal. Biochem., 201525 | 48 ScS samples (from 3 subjects) extracted in 100 mM AmBic, NaCl, a surfactant, or a combination of them at 25 °C for 4 h |
Offline SCX fractionation of peptides (16 fractions) |
LTQ-Orbitrap XL hybrid |
Peptide and protein with FDRs of < 1% (high) and 5% (relaxed) LTQ-Orbitrap |
1526 | |
| Dor et al., Exp. Eye Res., 201923 | 16 ScS samples (from 8 subjects) centrifuged at 7840 g for 7 min at 4 °C with no additional buffer |
Off-gel electrophoresis of peptides (12 fractions) |
LTQ-Orbitrap Velos Pro TripleTOF 5600 + in SWATH-MS mode |
Two unique peptides, FDR < 1% |
1351 | |
| Nättinen et al., Trans. Vis. Sci. Tech., 202030 | 31 ScS samples (from 31 subjects) incubated in 50 mM AmBic on ice for 60 min | In-solution digestion of whole samples (no pre-fractionation) |
TripleTOF 5600 + in SWATH-MS mode |
FDR < 1% | 908 | |
| Akkurt Arslan et al. Metabolites, 202128 |
8 ScS samples (from 2 subjects) extracted in 100 mM ammonium bicarbonate at 4 °C for 4 h |
In-solution digestion of whole samples (no pre-fractionation) | TimsTOF Pro | FDR < 1% | 1582 |
The studies included for the analysis of enzymes in this study collected tear samples using the capillary method or Schirmer strips. These studies report comprehensive datasets of the healthy human tear proteome, and all of them used mass spectrometry.
FDR false discovery rate, SCX strong cation exchange, ScS Schirmer strips, AmBic ammonium bicarbonate.