| Literature DB >> 32476319 |
Jia San Zheng1, Ren Yue Wei1, Zheng Wang1, Ting Ting Zhu1, Hong Ri Ruan1, Xue Wei1, Kai Wen Hou1, Rui Wu2.
Abstract
BACKGROUND: Feline mammary carcinoma is the third most common cancer that affects female cats.Entities:
Keywords: Feline mammary carcinoma; PRM; label-free; proteomics
Year: 2020 PMID: 32476319 PMCID: PMC7263907 DOI: 10.4142/jvs.2020.21.e45
Source DB: PubMed Journal: J Vet Sci ISSN: 1229-845X Impact factor: 1.672
Experimental sample basic information
| Sample | Variety | Age | Gender | Spaying status | Tumor type | Disease stage |
|---|---|---|---|---|---|---|
| T-1 | Chinese pastoral cat | 5 | Female | Unspayed | Breast carcinoma | Without metastasis |
| T-2 | Chinese pastoral cat | 8 | Female | Unspayed | Breast carcinoma | Without metastasis |
| T-3 | Chinese pastoral cat | 7 | Female | Unspayed | Breast carcinoma | Without metastasis |
| T-4 | Chinese pastoral cat | 5 | Female | Unspayed | Breast carcinoma | Without metastasis |
| T-5 | Chinese pastoral cat | 9 | Female | Unspayed | Breast carcinoma | Without metastasis |
| T-6 | Chinese pastoral cat | 4 | Female | Unspayed | Breast carcinoma | Without metastasis |
| C-1 | Chinese pastoral cat | 6 | Female | Unspayed | - | - |
| C-2 | Chinese pastoral cat | 7 | Female | Unspayed | - | - |
| C-3 | Chinese pastoral cat | 9 | Female | Unspayed | - | - |
| C-4 | Chinese pastoral cat | 5 | Female | Unspayed | - | - |
| C-5 | Chinese pastoral cat | 8 | Female | Unspayed | - | - |
| C-6 | Chinese pastoral cat | 4 | Female | Unspayed | - | - |
Search parameters
| Item | Values |
|---|---|
| Main search ppm | 6 |
| Missed cleavage | 2 |
| MS/MS tolerance ppm | 20 |
| De-isotopic | True |
| Enzyme | Trypsin |
| Database | Felinae |
| Fixed modification | Carbamidomethyl (C) |
| Variable modification | Oxidation (M), Acetyl (Protein N-term) |
| Decoy database pattern | Reverse |
| LFQ | True |
| LFQ min ratio count | 1 |
| Match between runs | 2 min |
The results filtering parameter was a peptide FDR ≤ 0.01.
LFQ, label-free quantification; FDR, false discovery rate.
List of differential protein
| Accession | Gene name | Ratio (T/C) | p value | Sig (T/C) |
|---|---|---|---|---|
| M5AXY1 | 0.340154831 | 0.005468144 | −1 | |
| P19707 | 0.054343484 | 0.000288975 | −1 | |
| M3VUN8 | 0.484964825 | 0.001937821 | −1 | |
| Q6SA95 | 0.508561675 | 0.011208751 | −1 | |
| M3VV12 | 0.433581397 | 0.000846272 | −1 | |
| M3VYX8 | 0.054318521 | 0.002185755 | −1 | |
| M3W922 | 0.039875786 | 0.00162386 | −1 | |
| M3W9M0 | 0.623818382 | 0.000846481 | −1 | |
| M3WAT6 | 0.244947483 | 0.000547107 | −1 | |
| M3WCX6 | 0.472553687 | 0.006494813 | −1 | |
| M3WFT4 | 0.254585428 | 0.003848397 | −1 | |
| M3WG98 | 0.338539837 | 0.000413087 | −1 | |
| M3WKC7 | 0.589201352 | 0.001317432 | −1 | |
| M3WYZ8 | 0.444775417 | 0.022068764 | −1 | |
| M3WN61 | 0.598273187 | 0.002881156 | −1 | |
| M3WN87 | 0.154237646 | 1.31441E-05 | −1 | |
| M3WNX1 | 0.265080498 | 0.001790853 | −1 | |
| M3WZC2 | 0.119091719 | 0.000846624 | −1 | |
| M3X116 | 0.294465392 | 0.008850929 | −1 | |
| M3X6U7 | 0.563686709 | 0.000238362 | −1 | |
| M3XAB5 | 0.47045168 | 0.003733989 | −1 | |
| M3W955 | 0.645298212 | 0.000358232 | −1 | |
| M3VWC6 | 0.584999947 | 0.007776608 | −1 | |
| M3VWV2 | 0.506921572 | 0.046079809 | −1 | |
| M3VZ45 | 0.30524973 | 0.022085741 | −1 | |
| M3W9I5 | 0.655991477 | 0.020887897 | −1 | |
| M3WAY1 | 0.319637263 | 0.041152642 | −1 | |
| M3WB06 | 0.360201549 | 5.61189E-05 | −1 | |
| M3WCW9 | 0.00420552 | 3.88075E-08 | −1 | |
| M3WCX4 | 0.645490262 | 0.007234816 | −1 | |
| M3WEG4 | 0.629841982 | 0.000223236 | −1 | |
| M3WEJ3 | 0.52457714 | 0.015276461 | −1 | |
| M3WFU5 | 0.633298239 | 0.027278073 | −1 | |
| M3WHB2 | 0.544596167 | 0.025876344 | −1 | |
| M3WJK3 | 0.60350631 | 0.01046831 | −1 | |
| M3XC93 | 0.597941906 | 0.009007362 | −1 | |
| M3WKJ1 | 0.53966298 | 0.043554677 | −1 | |
| M3WMF1 | 0.583225783 | 0.017732428 | −1 | |
| M3WNF1 | 0.614679704 | 0.000325913 | −1 | |
| M3WNL1 | 0.390329187 | 0.000912172 | −1 | |
| M3WSC8 | 0.045088855 | 0.042092242 | −1 | |
| M3WZ75 | 0.618899644 | 0.000233478 | −1 | |
| M3X096 | 0.550054256 | 0.018068838 | −1 | |
| M3X8P7 | 0.18635496 | 0.002091716 | −1 | |
| M3X9R6 | 0.469251471 | 0.002458933 | −1 | |
| M3XAV0 | 0.589338131 | 0.01171963 | −1 | |
| P07405 | 0.503946462 | 0.003003589 | −1 | |
| P07412 | 0.119153625 | 0.012125021 | −1 | |
| M3W3J4 | 0.304828166 | 0.002103913 | −1 | |
| M3W949 | 0.445288076 | 0.020020294 | −1 | |
| M3WF45 | 0.252986799 | 0.038081664 | −1 | |
| M3WGM9 | 0.229665329 | 0.007372795 | −1 | |
| M3WND9 | 0.478588155 | 0.000121836 | −1 | |
| M3WT57 | 0.12729283 | 0.000135858 | −1 | |
| M3XFW7 | 0.55652626 | 0.000805583 | −1 | |
| M3WN28 | 8.446550951 | 5.44584E-05 | 1 | |
| P14450 | 24.00986865 | 8.8154E-06 | 1 | |
| A0A0A0MQ10 | 3.006122799 | 0.018135641 | 1 | |
| M3W022 | 52.60613479 | 2.79305E-06 | 1 | |
| M3W285 | 1.805260304 | 0.000675015 | 1 | |
| M3W3E7 | 1.637796598 | 0.001506633 | 1 | |
| M3W3L1 | 45.511574 | 0.001091684 | 1 | |
| M3WCL4 | 1.626557922 | 0.012816445 | 1 | |
| M3WF07 | 2.198814542 | 0.005486296 | 1 | |
| M3WS14 | 16.90172405 | 0.000362214 | 1 | |
| M3WS63 | 1.792088653 | 0.003957038 | 1 | |
| M3WUF8 | 1.683414605 | 0.02320278 | 1 | |
| M3X1D8 | 2.019029718 | 0.040168563 | 1 | |
| M3X2G1 | 1.657819485 | 0.002520486 | 1 | |
| M3X4B4 | 1.608082992 | 0.025560436 | 1 | |
| M3X4U4 | 1.71662824 | 0.035243888 | 1 | |
| M3X8D0 | 2.120704462 | 0.003983756 | 1 | |
| M3XAZ9 | 3.66814103 | 0.003153746 | 1 | |
| M3XBL5 | 1.718928362 | 0.002066203 | 1 | |
| M3XBM6 | 1.559017816 | 0.03476085 | 1 | |
| M3XG21 | 1.791676147 | 0.00174948 | 1 | |
| M3XG22 | 2.983686145 | 0.001869249 | 1 | |
| M3VUY9 | 1.662661959 | 0.005309183 | 1 | |
| M3WFB3 | 1.582380649 | 0.010907316 | 1 | |
| M3WII3 | 128.4162109 | 2.11552E-07 | 1 | |
| M3XES3 | 1.572430224 | 0.017941538 | 1 | |
| M3X833 | 1.629792726 | 0.003791816 | 1 |
Sig (T/C) = 1 means this protein was up-regulated in group T compared with group C; Sig (T/C) = −1 means this protein was reduce in group T compared with group C.
Fig. 1Differential protein volcano map.
GO analysis
| Gene ontology | GO term | GO term ID | Proteins |
|---|---|---|---|
| Cellular component | Extracellular region | GO:0005576 | |
| Nucleus | GO:0005634 | ||
| Cytoplasm | GO:0005737 | ||
| Membrane | GO:0016020 | ||
| Plasma membrane | GO:0005886 | ||
| Molecular function | Receptor binding | GO:0005102 | |
| Metal ion binding Categories | GO:0046872 | ||
| Biological process | Immune system process | GO:0002376 | |
| Membrane organization | GO:0061024 | ||
| Signal transduction | GO:0007165 | ||
| Vesicle-mediated transport | GO:0016192 |
GO, gene ontology.
Fig. 2Differential protein GO. The x-coordinate represents the cell components of GO Slim, the y-coordinate histogram is the number of proteins, and the red line is the enrichment degree of each cell component. (A) cellular component, (B) Molecular function, (C) Biological process.
GO, gene ontology.
Fig. 3KEGG analysis. (A) Analysis of KEGG pathways for differentially expressed proteins. (B) The number of up-regulated and down-regulated proteins. The abscissa represents KEGG entries, the ordinate histogram is the number of proteins, and the red line is the enrichment of each KEGG entry.
KEGG, Kyoto Encyclopedia of Genes and Genomes.
List of differential proteins
| Gene name | Description | Ratio (T/C) |
|---|---|---|
| Apolipoprotein A-II | 0.15 | |
| Apolipoprotein C-III | 0.045 | |
| Apolipoprotein B | 0.50 | |
| Apolipoprotein A-IV | 0.65 |
Fig. 4Screening of protein-protein interaction network for differentially expressed proteins.
Parallel reaction monitoring protein concentration
| Sample No | Sample concentration (μg/uL) | Sample volume (μL) | Total protein (μg) | Whether it meets the experimental requirements |
|---|---|---|---|---|
| C | 24.27 | 1,000 | 24,268.92 | Meet |
| T | 26.29 | 1,000 | 26,291.47 | Meet |
Parallel reaction monitoring and label-free protein expression
| Protein name | PRM protein expression ratio (T/C) | Label free protein expression ratio (T/C) |
|---|---|---|
| 0.384125116 | 0.502469215 | |
| 0.389446911 | 0.045088854 | |
| 0.351008361 | 0.154237646 | |
| 0.041418351 | 0.360201549 | |
| Uncharacterized protein | 0.720178648 | 0.635512035 |
| 0.886057883 | 0.851275633 |