Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples
Abstract
:1. Introduction
2. Results
2.1. Peptide Extraction Methods and Sample Handling
2.2. Comparison of the Peptidome Composition of Salivary Gland Extracts and Saliva
2.3. Bioinformatic Analysis
2.4. Possible Peptide Biomarkers of Salivary Gland Tumors
2.5. Saliva-Specific Proteins
3. Discussion
4. Materials and Methods
4.1. Salivary Gland Tissue Collection
4.2. Saliva Samples Collection
4.3. Isolation of Peptide Fractions from Salivary Gland Tissue
4.4. Peptide Isolation from Saliva
4.5. LC-MS/MS
4.6. Exploratory Data Analysis
4.7. Ethics Committee Approval and Personal Data Handling
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Salivary Gland Tissue Samples | |||||
---|---|---|---|---|---|
Fresh | Frozen | Total | |||
PBS | TFA | PBS | TFA | ||
Tumor | 5 | 4 | 5 | 4 | 18 |
Control | 5 | 4 | 5 | 4 | 18 |
Total | 10 | 8 | 10 | 8 | 36 |
Saliva Samples | |||||
Patient | Control | Total | |||
11 | 8 | 19 |
Data Sets | Peptides | Unique Peptides | Stand-Alone Peptides |
---|---|---|---|
SG tumor | 8233 | 3916 | 1733 |
SG control | 3515 | 1586 | 589 |
SG fresh | 6752 | 3205 | 1383 |
SG frozen | 6913 | 3212 | 1496 |
SG PBS | 7771 | 3649 | 1667 |
SG TFA | 3540 | 1770 | 702 |
SG All | 10,380 | 4869 | 2077 |
Saliva patient | 3201 | 1166 | 325 |
Saliva control | 2461 | 836 | 258 |
Saliva all | 4189 | 1490 | 420 |
Data Sets | Overlapping Sequences | Common Peptides |
---|---|---|
Saliva patient—SG tumor | 377 | 86 |
Saliva patient only—SG tumor only | 109 | 16 |
Saliva patient—SG control | 960 | 182 |
Saliva patient only—SG control only | 362 | 42 |
Saliva control—SG tumor | 425 | 121 |
Saliva control only—SG tumor only | 154 | 39 |
Saliva control—SG control | 950 | 209 |
Saliva control only—SG control only | 351 | 58 |
Protein Accession | Protein Name | Gene Names | No. Peptides |
---|---|---|---|
P63261, P60709 | Actin, cytoplasmic | ACTB, ACTG | 9 |
P01009 | Alpha-1-antitrypsin | SERPINA1 | 1 |
P04083 | Annexin A1 | ANXA1 | 3 |
V9GYC1 | Apolipoprotein A-II | APOA2 | 1 |
P04280, P02812, Q04118, P10163 | Basic salivary proline-rich proteins | PRB1/4 | 32 |
Q96DR5 | BPI fold-containing family A member 2 (SPLUNC2, Parotid secretory protein) | BPIFA2 | 1 |
P04080 | Cystatin-B | CSTB | 1 |
P02671 | Fibrinogen alpha chain | FGA | 2 |
P02675 | Fibrinogen beta chain | FGB | 2 |
P09211 | Glutathione S-transferase P | GSTP1 | 3 |
P04406 | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) | GAPDH | 4 |
P04792 | Heat shock protein beta-1 | HSPB1 | 2 |
P69905, P68871 | Hemoglobin | HBA1/HBA2, HBB | 5 |
P16402, P10412, P16401, P20671 | Histones | H1-3, H1-4, H1-5, H2AC7 | 9 |
P01857 | Immunoglobulin heavy constant gamma 1 | IGHG1 | 1 |
P04264, P13647 | Keratin | KRT1, KRT5 | 4 |
Q09666 | Neuroblast differentiation-associated protein AHNAK (Desmoyokin) | AHNAK | 2 * |
P05109 | Protein S100-A8 (Calgranulin-A) | S100A8 | 2 |
P06702 | Protein S100-A9 (Calgranulin-B) | S100A9 | 2 |
Q08188 | Protein-glutamine gamma-glutamyltransferase E | TGM3 | 1 |
P02810 | Salivary acidic proline-rich phosphoprotein 1/2 | PRH1; PRH2 | 17 |
P62328 | Thymosin beta-4 | TMSB4X | 2 (1 **) |
P60174 | Triosephosphate isomerase | TPI1 | 2 |
P08670 | Vimentin | VIM | 1 |
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Puchalski, M.; Tretiakow, D.; Skorek, A.; Szydłowski, K.; Stodulski, D.; Mikaszewski, B.; Odroniec, A.; Musiał, N.; Thiel, M.; Czaplewska, P.; et al. Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples. Int. J. Mol. Sci. 2024, 25, 8799. https://doi.org/10.3390/ijms25168799
Puchalski M, Tretiakow D, Skorek A, Szydłowski K, Stodulski D, Mikaszewski B, Odroniec A, Musiał N, Thiel M, Czaplewska P, et al. Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples. International Journal of Molecular Sciences. 2024; 25(16):8799. https://doi.org/10.3390/ijms25168799
Chicago/Turabian StylePuchalski, Michał, Dmitry Tretiakow, Andrzej Skorek, Konrad Szydłowski, Dominik Stodulski, Bogusław Mikaszewski, Amadeusz Odroniec, Natalia Musiał, Marcel Thiel, Paulina Czaplewska, and et al. 2024. "Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples" International Journal of Molecular Sciences 25, no. 16: 8799. https://doi.org/10.3390/ijms25168799