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Figure S1. Default DanteR R-rollup menu

Figure S2. Default DanteR Z-rollup menu

Figure S3. Statistical processing of the human diabetes peptide abundance data

Figure S4. Statistical processing of the mouse lung tissue peptide abundance data

Figure S5. Protein abundance estimates for mouse protein 1433B

Table S1. Matlab scripts for protein quantification methods u-REF1 and u-REF2

Table S2. R script for protein quantification method LM2

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