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...
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Elsevier
2015-09-01
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| Series: | EuPA Open Proteomics |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S221296851530012X |
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doaj-17bd82b45234479db4d1d2fe726c072d2020-11-24T21:54:16ZengElsevierEuPA Open Proteomics2212-96852015-09-018C788410.1016/j.euprot.2015.07.011Workflow for large-scale analysis of melanoma tissue samplesMaria E. Yakovleva0Charlotte Welinder1Yutaka Sugihara2Krzysztof Pawłowski3Melinda Rezeli4Elisabet Wieslander5Johan Malm6György Marko-Varga7Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, SwedenOncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, SwedenOncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, SwedenDept. of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, PolandClinical Protein Science & Imaging, Dept. of Biomedical Engineering, Lund University, Lund, SwedenOncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, SwedenSection for Clinical Chemistry, Dept. of Laboratory Medicine, Lund University, Skåne University Hospital in Malmö, Malmö, SwedenClinical Protein Science & Imaging, Dept. of Biomedical Engineering, Lund University, Lund, SwedenThe 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.http://www.sciencedirect.com/science/article/pii/S221296851530012XMelanomaShotgun proteomicsData-dependent acquisition (DDA)TissueSample preparationDatabase |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Maria E. Yakovleva Charlotte Welinder Yutaka Sugihara Krzysztof Pawłowski Melinda Rezeli Elisabet Wieslander Johan Malm György Marko-Varga |
| spellingShingle |
Maria E. Yakovleva Charlotte Welinder Yutaka Sugihara Krzysztof Pawłowski Melinda Rezeli Elisabet Wieslander Johan Malm György Marko-Varga Workflow for large-scale analysis of melanoma tissue samples EuPA Open Proteomics Melanoma Shotgun proteomics Data-dependent acquisition (DDA) Tissue Sample preparation Database |
| author_facet |
Maria E. Yakovleva Charlotte Welinder Yutaka Sugihara Krzysztof Pawłowski Melinda Rezeli Elisabet Wieslander Johan Malm György Marko-Varga |
| author_sort |
Maria E. Yakovleva |
| title |
Workflow for large-scale analysis of melanoma tissue samples |
| title_short |
Workflow for large-scale analysis of melanoma tissue samples |
| title_full |
Workflow for large-scale analysis of melanoma tissue samples |
| title_fullStr |
Workflow for large-scale analysis of melanoma tissue samples |
| title_full_unstemmed |
Workflow for large-scale analysis of melanoma tissue samples |
| title_sort |
workflow for large-scale analysis of melanoma tissue samples |
| publisher |
Elsevier |
| series |
EuPA Open Proteomics |
| issn |
2212-9685 |
| publishDate |
2015-09-01 |
| description |
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. |
| topic |
Melanoma Shotgun proteomics Data-dependent acquisition (DDA) Tissue Sample preparation Database |
| url |
http://www.sciencedirect.com/science/article/pii/S221296851530012X |
| work_keys_str_mv |
AT mariaeyakovleva workflowforlargescaleanalysisofmelanomatissuesamples AT charlottewelinder workflowforlargescaleanalysisofmelanomatissuesamples AT yutakasugihara workflowforlargescaleanalysisofmelanomatissuesamples AT krzysztofpawłowski workflowforlargescaleanalysisofmelanomatissuesamples AT melindarezeli workflowforlargescaleanalysisofmelanomatissuesamples AT elisabetwieslander workflowforlargescaleanalysisofmelanomatissuesamples AT johanmalm workflowforlargescaleanalysisofmelanomatissuesamples AT gyorgymarkovarga workflowforlargescaleanalysisofmelanomatissuesamples |
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