Workflow for large-scale analysis of melanoma tissue samples

Maria E. Yakovleva, Charlotte Welinder, Yutaka Sugihara, Krzysztof Pawłowski, Melinda Rezeli, Elisabet Wieslander, Johan Malm, György Marko-Varga

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)78-84
Number of pages7
JournalEuPA Open Proteomics
Volume8
DOIs
StatePublished - Sep 1 2015
Externally publishedYes

Keywords

  • Data-dependent acquisition (DDA)
  • Database
  • Melanoma
  • Sample preparation
  • Shotgun proteomics
  • Tissue

ASJC Scopus subject areas

  • Biochemistry

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