Workflow for large-scale analysis of melanoma tissue samples

Publication date: Available online 10 July 2015 Source:EuPA Open Proteomics Author(s): Maria E. Yakovleva , Charlotte Welinder , Yutaka Sugihara , Krzysztof Pawłowski , Melinda Rezeli , Elisabet Wieslander , Johan Malm , György Marko-Varga The aim of the present study was to create an optimal workflow for analysing a large cohort of malignant melanoma tissue samples. Samples were lysed with urea and enzymatically digested with trypsin or trypsin/Lys C. Buffer exchange or dilution was used to reduce urea concentration prior to digestion. The tissue digests were analysed directly or following strong cation exchange (SCX) fractionation by nanoLC-MS/MS. The approach which resulted in the largest number of protein IDs involved a buffer exchange step before enzymatic digestion with trypsin and chromatographic separation in 120min gradient followed by SCX-RP separation of peptides. Graphical abstract
Source: EuPA Open Proteomics - Category: Bioinformatics Source Type: research