1. Supplemental figure 1. Supplemental Figure 1. Representative histology of human FFPE pancreas. This figure represents typical areas of the tissues from which proteins for this study were extracted (all panels are H&E, original magnification x 200). A.A typical case of chronic pancreatitis from a patient without PDAC. Arrows demarcate remaining epithelial and inflammatory cells typical of advanced chronic pancreatitis. This specimen was not used in the study, but was adjacent to uninvolved tissue used. B.Relatively normal-appearing pancreas (i.e. uninvolved). Arrows demarcate islets. C.Typical of the PDAC9. Arrows demonstrate a focus of PDAC. D.Typical of the PDAC7. Arrows demonstrate a focus of PDAC. E.Typical of the PDAC4. Arrows demonstrate a focus of PDAC. F.Typical of the PDAC5. Arrows demonstrate a focus of PDAC.

2. Supplemental Figure 2. Supplemental figure 2. Mouse tissue lysate separated with 1D-PAGE. Five micrograms of lysate per sample was separated on a 4-12% gel at 125V constant for 15min. The band indicated with parentheses was excised and subjected for analysis. FFPE; FFPE mouse pancreas tissues. Frozen; matched frozen pancreas tissues. Each lane corresponds to lysate from each individual animal (n=8). Standard; protein molecular weight marker (3-188 kDa), which guided us to determine the front line of the separation. FFPE Frozen Marker rep1rep2rep3rep4rep5rep6rep7rep8

3. Supplemental figure 3. A.B. FFPE Frozen FFPE Frozen Supplemental figure 3. Gene ontology (GO) analysis A.Cellular localization of identified proteins. B.Molecular Function of identified proteins.

4. 1734 FFPEFrozen/M-per 12 Frozen/FFPE 178 17 42 25 Supplemental Figure 4. Supplemental figure 4. Comparison of the number of protein identifications in FFPE vs. two different lysis methods of matched frozen tissues. Strict Venn diagram shows the overlap in number of proteins identified in FFPE (FFPE), matched frozen tissues prepared with a conventional lysis method (Frozen/M-per), and matched frozen tissues prepared with the Qproteome FFPE Tissue kit (Frozen/FFPE). The number shown are the total numbers identified in eight individual animal tissues.

5. Supplemental Table 1: Patient Information for Human FFPE Tissues Note*: AA: African American, CA: European American, N/A: Not Available. **: M: Male, F: Female.

6. Supplemental Table 2: Proteins Increased in PDAC Note: Instrumentation; Thermo Scientific LTQ-XL. Protein identifications with confidence >95%.

7. Note: Instrumentation; Thermo Scientific LTQ-XL. Protein identifications with >95% confidence. Supplemental Table 3: Proteins Decreased in PDAC