Additional file 2 of Comparative analysis of differentially abundant proteins quantified by LC–MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples

Additional file 2: Table S1. Percentage of tumor and stroma in each OCT/LMD sample before and after laser microdissection. Table S2. Number of proteins quantified in each sample. Table S3. Differentially expressed proteins between FF/HOM and OCT/LMD-T. Table S4. Differentially expressed proteins between FF/HOM and OCT/LMD-TS. Table S5. Differentially expressed proteins common between FF/HOM vs OCT/LMD-T and FF/HOM vs. OCT/LMD-TS. Table S6. Differentially enriched GO Terms between FF/HOM and OCT/LMD-T. Table S7. Differentially enriched GO Terms between FF/HOM and OCT/LMD-TS. Table S8. Differentially enriched GO Terms common between FF/HOM vs OCT/LMD-T and FF/HOM vs. OCT/LMD-TS. Table S9. Non-significant differentially expressed proteins between OCT/LMD-T and OCT/LMD-TS. Table S10. Non-significant differentially enriched GO Terms between OCT/LMD-T and OCT/LMD-TS. Table S11. Trended differentially expressed proteins between OCT/LMD-T and OCT/LMD-TS using paired analysis. Table S12. Differentially enriched GO Terms between OCT/LMD-T and OCT/LMD-TS using paired analysis. Table S13. Select stroma-associated GO terms from Table S12 and the proteins from Table S11 that map to them.