Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Sample Preparation
2.2.1. Acetone Precipitation
2.2.2. In-Solution Digestion
2.2.3. Filter-Aided Digestion (FASP)
2.2.4. ProteoMiner Enrichment
2.2.5. SDS-PAGE Fractionation and In-Gel Digestion
2.2.6. Acetonitrile Precipitation
2.2.7. Desalting
2.3. Mass Spectrometry
2.3.1. Data-Dependent Acquisition (DDA)
2.3.2. Spectral Library Construction
2.3.3. Data-Independent Acquisition
2.3.4. Quantitative Analysis
3. Results
3.1. Protein Identifications from Different Digestion Techniques
3.2. Protein Identifications from Different Sample Types
3.3. Protein Identifications after ProteoMiner
3.4. Protein Identifications after ACN Precipitation
3.5. Protein Quantitation Using Data-Independent Acquisition
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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No. | Condition | No. of Animals Used to Generate a Pooled Sample | Digestion Technique | Fractionation/Enrichment Technique |
---|---|---|---|---|
1 | Healthy | 8 |
|
|
2 | Unhealthy (inflammatory and miscellaneous conditions) | 26 | Filter-aided | None |
No. | Condition | No. of Animals Used to Generate a Pooled Sample | Digestion Technique | Fractionation/Enrichment Technique |
---|---|---|---|---|
1 | Healthy | 8 | Filter-aided | None |
2 | Inflammatory conditions | 8 | Filter-aided | None |
3 | Miscellaneous conditions | 18 | Filter-aided | None |
Sl. No. | Disease Condition | Proteins Studied | Reference |
---|---|---|---|
1 | Canine Babesiosis | Alpha 1 acid glycoprotein, Apolipoprotein A-1, Complement c3, Hemopexin, Alpha 2-HS glycoprotein, Haptoglobin, Clusterin | [43] |
2 | Canine lymphoma | Apolipoprotein A-I, Apolipoprotein C-I, Apolipoprotein C-II, Apolipoprotein C-III, Apolipoprotein E, Beta-2-glycoprotein 1, Clusterin, Coagulation factor IX, Fibrinogen alpha chain, Fibrinogen beta chain (Fragment), Fibrinogen gamma chain Fibronectin, Haptoglobin, Plasminogen Serum amyloid A protein, Transferrin receptor protein 1 | [44] |
4 | Canine Pyometra | Alpha-1-acid glycoprotein 1, Haptoglobin, Alpha-2-macroglobulin, Hemopexin, Transthyretin, Transferrin receptor protein, Retinol-binding protein, Gelsolin, Alpha 2-HS glycoprotein | [45] |
5 | Canine Mammary tumors | Alpha-1-microglobulin/bikunin precursor, Angiotensinogen, Serum albumin, Gelsolin | [46] |
6 | Canine Chronic Valve disease | Apolipoprotein B, Apolipoprotein M, Apolipoprotein D | [47] |
7 | H3N2 canine Influenza virus | Haptoglobin, Apolipoprotein E, Alpha 1 acid glycoprotein, Beta-2-microglobulin | [48] |
8 | Duchenne muscular dystrophy | Alpha-1-B glycoprotein, Alpha 2-HS glycoprotein, Fetuin B, Hemopexin, Tropomyosin 2 | [49] |
10 | Canine Encephalitis | Hemopexin, Gelsolin, Transthyretin, Beta-2-glycoprotein 1 Apolipoprotein E | [50] |
11 | Canine Leishmaniasis | Haptoglobin, Hepatocyte growth factor activator, Hyaluronan binding protein 2 Sulfhydryl oxidase, Complement C8 alpha chain, Complement C9 | [24] |
Sl. No. | Protein Name | Human Disease Condition | Reference |
---|---|---|---|
1 | Gelsolin | Glioma | [51] |
2 | Ceruloplasmin | Identified as a protein biomarker in prostate cancer | [52] |
3 | Haptoglobin | Identified as biomarker in lung adeno carcinoma | [53] |
4 | Alpha 1 antitrypsin | Studied in human breast cancer | [54] |
5 | Vimentin | Expressed in human and canine osteosarcoma cells | [55] |
6 | Tropomyosin 3 | Upregulated in metastatic carcinomas | [56] |
7 8 | Myosin light chain 2 Tropomyosin 1 | Downregulated in metastatic mammary carcinoma, which is also expressed in human breast cancer | |
9 | Triosephosphate isomerase | Analysed as autoantigens from the canine mammary cell line | [57] |
10 11 | Transthyretin Apolipoprotein A-I | Identified as biomarkers for detecting early stage of ovarian cancer in human | [58] |
12 | Tissue inhibitor of metalloproteinase 1 (Fragment) | Pancreatic cancer | [59] |
13 | Alpha 2-HS glycoprotein Transthyretin | Colorectal cancer | [60] |
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Ravuri, H.G.; Noor, Z.; Mills, P.C.; Satake, N.; Sadowski, P. Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. Proteomes 2022, 10, 9. https://doi.org/10.3390/proteomes10010009
Ravuri HG, Noor Z, Mills PC, Satake N, Sadowski P. Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. Proteomes. 2022; 10(1):9. https://doi.org/10.3390/proteomes10010009
Chicago/Turabian StyleRavuri, Halley Gora, Zainab Noor, Paul C. Mills, Nana Satake, and Pawel Sadowski. 2022. "Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma" Proteomes 10, no. 1: 9. https://doi.org/10.3390/proteomes10010009
APA StyleRavuri, H. G., Noor, Z., Mills, P. C., Satake, N., & Sadowski, P. (2022). Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. Proteomes, 10(1), 9. https://doi.org/10.3390/proteomes10010009