Workflow for large-scale analysis of melanoma tissue samples

Workflow for large-scale analysis of melanoma tissue samples

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 digestio...

Full description

Bibliographic Details
Main Authors: Maria E. Yakovleva, Charlotte Welinder, Yutaka Sugihara, Krzysztof Pawłowski, Melinda Rezeli, Elisabet Wieslander, Johan Malm, György Marko-Varga
Format: Article
Language:English
Published: Elsevier 2015-09-01
Series:EuPA Open Proteomics
Subjects:
Melanoma
Shotgun proteomics
Data-dependent acquisition (DDA)
Tissue
Sample preparation
Database
Online Access:http://www.sciencedirect.com/science/article/pii/S221296851530012X
Description
Summary: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 nano LC–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 120 min gradient followed by SCX–RP separation of peptides.
ISSN:2212-9685

Similar Items