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 |
