Comparative Label-Free Liquid Chromatography–Mass Spectrometry Milk Proteomic Profiles Highlight Putative Differences between the Autochthon Teramana and Saanen Goat Breeds
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Sample Preparation
2.3. Filter-Aided Sample Preparation (FASP)
2.4. Mass Spectrometry for Label-Free LC–MS
2.5. Label-Free LC–MS Quantitative Profiling
2.6. Functional and Protein Network Analyses
3. Results
3.1. Identification of Milk Proteins in Goat Breeds
3.2. Label-Free Quantitative Proteomic Analysis of Goat Milk
3.3. Functional Association Analysis
3.4. Protein–Protein Interaction (PPI) Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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UniProt * | Gene Name | Description | Peptides § | Score ¥ | ANOVA (p) | Fold Change | Highest Condition ǂ |
---|---|---|---|---|---|---|---|
A0A452DX18 | C3 | Complement C3 | 27 | 94.92 | 0.0097 | 4.03 | Teramana |
A0A452F1G2 | THBS1 | Thrombospondin 1 | 9 | 24.44 | 0.0007 | 24.62 | Teramana |
A0A452DRX5 | PSAP | Prosaposin | 6 | 18.88 | 0.0031 | 2.63 | Teramana |
A0A452FHJ7 | GSN | Gelsolin | 6 | 20.57 | 0.0056 | 1.52 | Teramana |
A0A452E7A0 | PLG | Plasminogen | 6 | 22.23 | 0.0241 | 2.27 | Teramana |
A0A452FK23 | CSN2 | Beta-casein | 4 | 10.73 | 0.0086 | 2.06 | Teramana |
A0A452G9D9 | CSN3 | Kappa-casein | 4 | 36.55 | 0.0140 | 2.53 | Teramana |
A0A452E2Y0 | CLU | Clusterin | 4 | 15.79 | 0.0292 | 4.47 | Teramana |
D6PX62 | Crisp3 | Cysteine-rich secretory protein 3 | 3 | 9.86 | 0.0026 | 38.63 | Teramana |
A0A452G7V5 | P4HB | Protein disulfide-isomerase | 3 | 9.50 | 0.0245 | 2.12 | Teramana |
A0A452EZB5 | CD55 | Complement decay-accelerating factor | 3 | 7.99 | 0.0267 | 3.89 | Teramana |
A0A452F9Y8 | PPIB | Peptidyl-prolyl cis-trans isomerase | 3 | 10.26 | 0.0341 | 1.98 | Teramana |
A0A452GBG4 | CYR61 | Cellular communication network factor 1 | 2 | 7.98 | 0.0001 | 23.17 | Teramana |
A0A452EKN2 | IGHG4 | Immunoglobulin heavy constant gamma 4 | 2 | 6.11 | 0.0006 | 9.56 | Teramana |
A0A452DZD6 | rig-5 | Ig-like domain-containing protein | 2 | 8.56 | 0.0029 | 1.51 | Teramana |
A0A452G5W1 | GRN | Granulin precursor | 2 | 6.71 | 0.0034 | 3.02 | Teramana |
A0A452F4L3 | FGA | Fibrinogen alpha chain | 2 | 5.47 | 0.0194 | 2.46 | Teramana |
A0A452G077 | CTGF | Cellular communication network factor 2 | 2 | 6.67 | 0.0402 | 6.69 | Teramana |
A0A452EZW6 | XDH | FAD-binding PCMH-type domain-containing protein | 14 | 38.58 | 0.0089 | 1.96 | Saanen |
A0A452EYF6 | HSPA8 | Heat shock cognate 71 kDa protein | 5 | 15.53 | 0.0011 | 1.72 | Saanen |
A0A452ERT5 | SLC34A2 | Solute carrier family 34 member 2 | 4 | 9.43 | 0.0002 | 5.17 | Saanen |
A0A452E4K0 | CST6 | Cystatin E/M | 4 | 15.21 | 0.0041 | 2.86 | Saanen |
Q6S4N9 | FABP3 | Fatty acid binding protein 3 | 3 | 7.85 | 0.0002 | 1.75 | Saanen |
A0A452FN55 | BTN1A1 | Butyrophilin subfamily 1 member A1 | 3 | 8.43 | 0.0058 | 1.76 | Saanen |
A0A452F4U3 | FASN | Fatty acid synthase | 3 | 10.66 | 0.0104 | 4.12 | Saanen |
A0A452G9E6 | FOLR3 | Folate_rec domain-containing protein | 3 | 8.19 | 0.0164 | 1.83 | Saanen |
A0A452F3X9 | PROM2 | Prominin 2 | 2 | 5.84 | 0.0116 | 2.99 | Saanen |
A0A452E0U0 | CD81 | Tetraspanin | 2 | 13.07 | 0.0211 | 2.28 | Saanen |
A0A452F230 | NME1 | Nucleoside diphosphate kinase | 2 | 4.55 | 0.0320 | 1.52 | Saanen |
GOID | Description | Functional Group 1 | p-Value 2 | % of Associated Proteins 3 | No. of Proteins | Upregulated or Downregulated Proteins 4 |
---|---|---|---|---|---|---|
GO:0030879 | mammary gland development | G0 | 0.000057 | 3.88 | 4 | CSN2 ↓, CSN3 ↓, FASN ↑, XDH ↑ |
GO:0031647 | regulation of protein stability | G1 | 0.000053 | 2.56 | 5 | CD81 ↑, CLU ↓, CSN3 ↓, GSN ↓, PPIB ↓, |
GO:1903725 | regulation of phospholipid metabolic process | G2 | 0.003120 | 4.17 | 2 | CD81 ↑, FABP3 ↑ |
GO:0008543 | fibroblast growth factor receptor signalling pathway | G3 | 0.004663 | 3.17 | 2 | CTGF ↓, THBS1 ↓ |
GO:2000117 | negative regulation of cysteine-type endopeptidase activity | G4 | 0.006824 | 2.53 | 2 | CSN2 ↓, THBS1 ↓ |
GO:0009408 | response to heat | G5 | 0.004820 | 3.23 | 2 | CSN2 ↓, PLG ↓ |
GO:0010951 | negative regulation of endopeptidase activity | G6 | 0.000418 | 2.00 | 4 | C3 ↓, CSN2 ↓, CST6 ↑, THBS1 ↓ |
GO:0015909 | long-chain fatty acid transport | G7 | 0.003120 | 4.17 | 2 | FABP3 ↑, THBS1 ↓ |
GO:0019216 | regulation of lipid metabolic process | G8 | 0.000060 | 2.36 | 5 | C3 ↓, CD81 ↑, CYR61 ↓, FABP3 ↑, PSAP ↓ |
GO:0045834 | positive regulation of lipid metabolic process | G9 | 0.007858 | 2.22 | 2 | CD81 ↑, CYR61 ↓ |
GO:0045862 | positive regulation of proteolysis | G10 | 0.000071 | 2.09 | 5 | C3 ↓, CLU ↓, CYR61 ↓, GSN ↓, XDH ↑ |
GO:0046890 | regulation of lipid biosynthetic process | G11 | 0.000733 | 3.00 | 3 | C3 ↓, CYR61 ↓, FABP3 ↑ |
GO:0050821 | protein stabilisation | G12 | 0.001011 | 2.61 | 3 | CLU ↓, CSN3 ↓, PPIB ↓ |
GO:0060716 | labyrinthine layer blood vessel development | G13 | 0.000680 | 10.53 | 2 | CYR61 ↓, PLG ↓ |
GO:1903201 | regulation of oxidative stress-induced cell death | G14 | 0.003088 | 4.35 | 2 | P4HB ↓, PSAP ↓ |
GO:0019058 | viral life cycle | G15 | 0.000186 | 2.63 | 4 | CD81 ↑, GSN ↓, P4HB ↓, PPIB ↓ |
GO:1903900 | regulation of viral life cycle | G15 | 0.000186 | 3.06 | 3 | GSN ↓, P4HB ↓, PPIB ↓ |
GO:0052548 | regulation of endopeptidase activity | G16 | 0.000004 | 2.31 | 7 | C3 ↓, CSN2 ↓, CST6 ↑, CYR61 ↓, GSN ↓, THBS1 ↓, XDH ↑ |
GO:2000116 | regulation of cysteine-type endopeptidase activity | G16 | 0.000004 | 2.96 | 5 | CSN2 ↓, CYR61 ↓, GSN ↓, THBS1 ↓, XDH ↑ |
GO:0001937 | negative regulation of endothelial cell proliferation | G17 | 0.006928 | 7.14 | 2 | THBS1 ↓, XDH ↑ |
GO:2000181 | negative regulation of blood vessel morphogenesis | G17 | 0.006928 | 2.90 | 2 | THBS1 ↓, XDH ↑ |
GO:1903494 | response to dehydroepiandrosterone | G18 | 0.000390 | 40.00 | 2 | CSN2 ↓, CSN3 ↓ |
GO:0032570 | response to progesterone | G18 | 0.000390 | 15.38 | 2 | CSN2 ↓, CSN3 ↓ |
GO:1903496 | response to 11-deoxycorticosterone | G18 | 0.000390 | 40.00 | 2 | CSN2 ↓, CSN3 ↓ |
GO:0050878 | regulation of body fluid levels | G19 | 0.000014 | 2.48 | 6 | CSN2 ↓, CSN3 ↓, FGA ↓, PLG ↓, THBS1 ↓, XDH ↑ |
GO:0007596 | blood coagulation | G19 | 0.000014 | 2.07 | 3 | FGA ↓, PLG ↓, THBS1 ↓ |
GO:0032102 | negative regulation of response to external stimulus | G19 | 0.000014 | 2.00 | 4 | CSN2 ↓, FGA ↓, PLG ↓, THBS1 ↓ |
GO:1904019 | epithelial cell apoptotic process | G19 | 0.000014 | 4.69 | 3 | FGA ↓, GSN ↓, THBS1 ↓ |
GO:0016485 | protein processing | G19 | 0.000014 | 2.38 | 4 | C3 ↓, FGA ↓, GSN ↓, THBS1 ↓ |
GO:0006911 | phagocytosis, engulfment | G19 | 0.000014 | 10.00 | 3 | C3 ↓, GSN ↓, THBS1 ↓ |
GO:0042730 | fibrinolysis | G19 | 0.000014 | 15.79 | 3 | FGA ↓, PLG ↓, THBS1 ↓ |
GO:0070613 | regulation of protein processing | G19 | 0.000014 | 5.08 | 3 | C3 ↓, GSN ↓, THBS1 ↓ |
GO:1904035 | regulation of epithelial cell apoptotic process | G19 | 0.000014 | 6.52 | 3 | FGA ↓, GSN ↓, THBS1 ↓ |
GO:0031639 | plasminogen activation | G19 | 0.000014 | 8.70 | 2 | FGA ↓, THBS1 ↓ |
GOID | Description | Functional Group 1 | p-Value 2 | % of Associated Proteins 3 | No. of Proteins | Upregulated or Downregulated Proteins 4 |
---|---|---|---|---|---|---|
KEGG:04610 | Complement and coagulation cascades | G0 | 0.000004 | 5.56 | 5 | C3 ↓, CD55 ↓, CLU ↓, FGA ↓, PLG ↓ |
KEGG:05134 | Legionellosis | G1 | 0.013192 | 3.45 | 2 | C3 ↓, HSPA8 ↑ |
KEGG:05144 | Malaria | G2 | 0.009393 | 3.33 | 2 | CD81 ↑, THBS1 ↓ |
KEGG:05150 | Staphylococcus aureus infection | G3 | 0.009755 | 2.82 | 2 | C3 ↓, PLG ↓ |
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Di Luca, A.; Bennato, F.; Ianni, A.; Grotta, L.; Henry, M.; Meleady, P.; Martino, G. Comparative Label-Free Liquid Chromatography–Mass Spectrometry Milk Proteomic Profiles Highlight Putative Differences between the Autochthon Teramana and Saanen Goat Breeds. Animals 2023, 13, 2263. https://doi.org/10.3390/ani13142263
Di Luca A, Bennato F, Ianni A, Grotta L, Henry M, Meleady P, Martino G. Comparative Label-Free Liquid Chromatography–Mass Spectrometry Milk Proteomic Profiles Highlight Putative Differences between the Autochthon Teramana and Saanen Goat Breeds. Animals. 2023; 13(14):2263. https://doi.org/10.3390/ani13142263
Chicago/Turabian StyleDi Luca, Alessio, Francesca Bennato, Andrea Ianni, Lisa Grotta, Michael Henry, Paula Meleady, and Giuseppe Martino. 2023. "Comparative Label-Free Liquid Chromatography–Mass Spectrometry Milk Proteomic Profiles Highlight Putative Differences between the Autochthon Teramana and Saanen Goat Breeds" Animals 13, no. 14: 2263. https://doi.org/10.3390/ani13142263
APA StyleDi Luca, A., Bennato, F., Ianni, A., Grotta, L., Henry, M., Meleady, P., & Martino, G. (2023). Comparative Label-Free Liquid Chromatography–Mass Spectrometry Milk Proteomic Profiles Highlight Putative Differences between the Autochthon Teramana and Saanen Goat Breeds. Animals, 13(14), 2263. https://doi.org/10.3390/ani13142263