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

doi:10.1016/j.euprot.2015.07.011

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 journal › Article › peer-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 language	English (US)
Pages (from-to)	78-84
Number of pages	7
Journal	EuPA Open Proteomics
Volume	8
DOIs	https://doi.org/10.1016/j.euprot.2015.07.011
State	Published - Sep 1 2015
Externally published	Yes

Keywords

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

ASJC Scopus subject areas

Biochemistry

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10.1016/j.euprot.2015.07.011

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title = "Workflow for large-scale analysis of melanoma tissue samples",

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.",

keywords = "Data-dependent acquisition (DDA), Database, Melanoma, Sample preparation, Shotgun proteomics, Tissue",

author = "Yakovleva, {Maria E.} and Charlotte Welinder and Yutaka Sugihara and Krzysztof Paw{\l}owski and Melinda Rezeli and Elisabet Wieslander and Johan Malm and Gy{\"o}rgy Marko-Varga",

note = "Funding Information: This work was supported by grants from Mrs. Berta Kamprad Foundation , Swedish Academy of Pharmaceutical Sciences , Swedish Research Council , the Swedish Foundation for Strategic Research , Vinnova, Ingabritt & Arne Lundbergs forskningsstiftelse , and the Crafoord Foundation . M.Y. is thankful to Sven Kjellstr{\"o}m for useful advices and to Marcus Johansson for reviewing the manuscript. Publisher Copyright: {\textcopyright} 2015.",

year = "2015",

month = sep,

day = "1",

doi = "10.1016/j.euprot.2015.07.011",

language = "English (US)",

volume = "8",

pages = "78--84",

journal = "EuPA Open Proteomics",

issn = "2212-9685",

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}

TY - JOUR

T1 - Workflow for large-scale analysis of melanoma tissue samples

AU - Yakovleva, Maria E.

AU - Welinder, Charlotte

AU - Sugihara, Yutaka

AU - Pawłowski, Krzysztof

AU - Rezeli, Melinda

AU - Wieslander, Elisabet

AU - Malm, Johan

AU - Marko-Varga, György

N1 - Funding Information: This work was supported by grants from Mrs. Berta Kamprad Foundation , Swedish Academy of Pharmaceutical Sciences , Swedish Research Council , the Swedish Foundation for Strategic Research , Vinnova, Ingabritt & Arne Lundbergs forskningsstiftelse , and the Crafoord Foundation . M.Y. is thankful to Sven Kjellström for useful advices and to Marcus Johansson for reviewing the manuscript. Publisher Copyright: © 2015.

PY - 2015/9/1

Y1 - 2015/9/1

N2 - 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.

AB - 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.

KW - Data-dependent acquisition (DDA)

KW - Database

KW - Melanoma

KW - Sample preparation

KW - Shotgun proteomics

KW - Tissue

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SP - 78

EP - 84

JO - EuPA Open Proteomics

JF - EuPA Open Proteomics

ER -

Workflow for large-scale analysis of melanoma tissue samples

Abstract

Keywords

ASJC Scopus subject areas

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