Protein spots showing differential expression between genotype pools CIS-t and CIS-s before and/or after cold treatment. A virtual tuber protein pattern was generated by fusing 2D-PAGE gel images from both genotype pools CIS-t and CIS-s at T0. Conditions for protein separation in the first and second dimension are shown on the right. The numbered arrow heads point to the position of the 50 differential proteins described in Table 2, Additional file 4: Table S4 and Additional file 5: Table S5. (A) Proteins from 40 to 200 kDa were separated on IPG strips with immobilized pH gradient of 3–11 in the first dimension (IEF) and by 10% Tris-glycine SDS-PAGE in the second dimension. (B) Proteins between 5 and 40 kDa were separated on pH 3–7 IPG strips in the first dimension and by 16% Tris-tricine polyacrylamide gels in the second dimension.