Fig. 4
Analysis of luminal A-like and triple negative breast cancer samples by LMD-PAT-H-MS. a Heatmap display and nonsupervised clustering of the log2 of ratios obtained for the indicated hPTMs for microdissected luminal A-like and triple negative breast cancer samples, using LMD-PAT-H-MS (left) or the classical PAT-H-MS approach (right). L/H relative abundances ratios obtained with the super-SILAC strategy (light channel: breast cancer biopsy, heavy channel: spike-in super-SILAC standard) normalized over the average value across the samples are shown. Modified peptides significantly different in the two subtypes are indicated by asterisks. The grey color indicates peptides that were not quantified in the heavy channel or in both heavy and light channels, for which a L/H ratio could not be calculated. Encircled grey squares indicate peptides that were not quantified only in the light channel (L/H ratio = 0). b Ratios obtained for the indicated peptides in the luminal A-like or triple negative breast cancer samples shown in a. c Ratios obtained for the K9me3 peptide in frozen luminal A-like or triple negative breast cancer samples compared with their corresponding normal breast tissue. Five samples were analyzed in the top panel and three in the bottom one. Samples in b and c were compared by t test. Error bars represent standard error from three to six patient samples. *p < 0.05, **p < 0.01