Table 1. Top 50 most abundant transcripts/peptides in the mammary transcriptome and two milk proteomes.
| Rank | Early Lactation Mammary Transcriptome | % total | Early Lactation Milk Proteome | % total | Late Lactation Milk Proteome | % total |
|---|---|---|---|---|---|---|
| 1 | Beta-lactoglobulin | 8.19 | Beta-lactoglobulin | 15.59 | Lactotransferrin | 49.4 |
| 2 | Clusterin | 3.9 | Very early lactation protein | 13.3 | Beta-lactoglobulin | 10.53 |
| 3 | Alpha Casein | 3.16 | Zinc-alpha-2-glycoprotein | 7.1 | Ig alpha chain C region | 2.16 |
| 4 | KoRV | 3.13 | Haptoglobin | 5.46 | Immunoglobulin J chain | 1.96 |
| 5 | Keratin | 2.03 | Early lactation protein | 3.77 | Zinc-alpha-2-glycoprotein | 1.91 |
| 6 | Trichosurin | 2.02 | Whey acidic protein | 3.56 | Haptoglobin | 1.73 |
| 7 | Ferritin heavy chain | 1.55 | Trichosurin | 3.4 | Neutrophil gelatinase-associated lipocalin | 1.67 |
| 8 | Early lactation protein | 1.05 | Clusterin | 2.37 | Protein S100-A8 | 1.67 |
| 9 | Beta casein | 0.97 | Alpha-1-B glycoprotein-like | 1.48 | Lactadherin | 1.6 |
| 10 | Actin, cytoplasmic type 5 | 0.96 | Beta-casein | 1.44 | Beta-casein | 1.53 |
| 11 | Thymosin B-4 | 0.68 | Gelsolin | 1.44 | Trichosurin | 1.44 |
| 12 | Alpha-lactalbumin | 0.65 | Polymeric immunoglobulin receptor | 1.39 | Polymeric immunoglobulin receptor | 1.27 |
| 13 | Polyubiquitin-B | 0.63 | Complement C3 | 1.15 | Very early lactation protein | 1.25 |
| 14 | Kappa casein | 0.62 | Envelope glycoprotein (KoRV) | 0.97 | Hemoglobin subunit alpha | 1.07 |
| 15 | Butyrophilin subfamily 1 member A1 | 0.6 | Sulfhydryl oxidase 1 | 0.91 | Sulfhydryl oxidase 1 | 0.94 |
| 16 | 60S acidic ribosomal protein P1 | 0.47 | Complement C2 | 0.86 | Clusterin | 0.85 |
| 17 | Actin, aortic smooth muscle | 0.44 | Alpha-lactalbumin | 0.81 | Alpha-1-B glycoprotein-like | 0.74 |
| 18 | Nuclease EXOG, mitochondria | 0.44 | Alpha-casein | 0.77 | Vimentin | 0.74 |
| 19 | Zinc-alpha 2 glycoprotein | 0.43 | Alpha-1-antiproteinase | 0.75 | Alpha-enolase | 0.72 |
| 20 | Actin, cytoplasmic 1 | 0.41 | Lactadherin | 0.73 | Whey acidic protein | 0.72 |
| 21 | Insulin like growth factor | 0.38 | Neutrophil gelatinase-associated lipocalin | 0.71 | Nucleobindin-1 | 0.71 |
| 22 | Very early lactation protein | 0.36 | Hemoglobin subunit beta | 0.69 | Peptidyl-prolyl cis-trans isomerase A | 0.71 |
| 23 | Marsupial Milk 1 | 0.36 | Ig gamma chain C region | 0.68 | Transketolase | 0.6 |
| 24 | Actin, ACTM | 0.36 | Nucleobindin-1 | 0.64 | Peroxiredoxin-1 | 0.59 |
| 25 | Whey acidic protein | 0.34 | Hemoglobin subunit alpha | 0.55 | Protein S100-A9 | 0.59 |
| 26 | Cytochrome c | 0.32 | Marsupial milk 1 | 0.54 | Ig kappa chain C region | 0.58 |
| 27 | Transgelin | 0.31 | Actin, aortic smooth muscle | 0.52 | 78 kDa glucose-regulated protein | 0.56 |
| 28 | Matrix gla protein | 0.28 | 78 kDa glucose-regulated protein | 0.51 | Cathepsin L1 | 0.56 |
| 29 | 40S ribosomal protein S18 | 0.28 | Lipopolysaccharide-binding protein | 0.47 | Ig lambda chain V region | 0.51 |
| 30 | Secreted Protein, Acidic, Cysteine-Rich (Osteonectin) | 0.28 | Serum amyloid A protein | 0.46 | Phosphoglycerate mutase 1 | 0.51 |
| 31 | TCDD-inducible poly(ADP-ribose) polymerase | 0.26 | WAP four-disulfide core domain protein 2 | 0.45 | Actin, cytoplasmic 2 | 0.5 |
| 32 | Chain 5, 60s Rrna | 0.25 | Leucine-rich alpha-2-glycoprotein | 0.43 | Alpha-casein | 0.47 |
| 33 | 60S ribosomal protein L6 | 0.24 | Monocyte differentiation antigen CD14 | 0.42 | Ig gamma chain C region | 0.46 |
| 34 | Elongation factor-1 | 0.23 | Peroxiredoxin-1 | 0.41 | Kappa casein | 0.45 |
| 35 | Myosin light Polypeptide | 0.23 | Complement C4-A | 0.4 | Alpha-lactalbumin | 0.44 |
| 36 | Insulin-like growth factor-binding protein 5 | 0.23 | Alpha-2-macroglobulin | 0.38 | Protein disulfide-isomerase A3 | 0.44 |
| 37 | Collagen alpha-1(I) chain-like | 0.22 | Peroxidasin homolog | 0.38 | Insulin-like growth factor-binding protein 4 | 0.42 |
| 38 | Prostoglandin-H2 | 0.22 | Tumor necrosis factor receptor superfamily member 6B | 0.38 | Envelope glycoprotein (KoRV) | 0.4 |
| 39 | Putative ncRNA | 0.2 | Amyloid beta A4 protein | 0.36 | Ubiquitin-60S ribosomal protein L40 | 0.4 |
| 40 | Keratin | 0.2 | Elastin | 0.34 | Pigment epithelium-derived factor | 0.39 |
| 41 | 60S ribosomal protein L10a | 0.2 | Fibronectin | 0.34 | Profilin-1 | 0.39 |
| 42 | MHC class I | 0.2 | Cathepsin L1 | 0.32 | Marsupial milk 1 | 0.37 |
| 43 | 40S ribosomal protein S24 | 0.2 | C-C motif chemokine 3 | 0.29 | Gelsolin | 0.35 |
| 44 | Annexin A2 | 0.19 | Ceruloplasmin | 0.29 | Pro-Pol polyprotein (KoRV) | 0.3 |
| 45 | E3 ubiquitin | 0.19 | Prosaposin | 0.29 | Retinoic acid receptor responder protein 1 | 0.3 |
| 46 | Ribonuclease H1 | 0.18 | Fibroblast growth factor-binding protein 2 | 0.26 | Xanthine dehydrogenase/oxidase | 0.29 |
| 47 | 60S ribosomal protein L10 | 0.18 | Histone-lysine N-methyltransferase 2C | 0.25 | Dipeptidase 2 | 0.27 |
| 48 | Cysteine and glycine-rich protein 1 | 0.18 | Ig mu chain C region | 0.25 | Ig heavy chain V-III region VH26 | 0.27 |
| 49 | Prothymosin alpha | 0.18 | Peroxiredoxin-5, mitochondrial | 0.25 | Leukocyte elastase inhibitor | 0.27 |
| 50 | Vimentin | 0.17 | EGF-containing fibulin-like extracellular matrix protein 1 | 0.24 | Glucose-6-phosphate isomerase | 0.26 |
% total calculated as the percentage of total transcript expression/peptide abundance.