Sander R Piersma

Summary

Affiliation: VU University Medical Center
Country: The Netherlands

Publications

  1. pmc Whole gel processing procedure for GeLC-MS/MS based proteomics
    Sander R Piersma
    Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands
    Proteome Sci 11:17. 2013
  2. doi request reprint Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum
    Sander R Piersma
    OncoProteomics Laboratory, Department of Medical Oncology, VUMC Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
    J Proteome Res 9:1913-22. 2010
  3. ncbi request reprint Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues
    Jaco C Knol
    OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
    Biochim Biophys Acta 1844:1034-43. 2014
  4. doi request reprint Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression
    Meike de Wit
    Department of Pathology Tumor Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands
    Gut 61:855-64. 2012
  5. pmc Proteomics of genetically engineered mouse mammary tumors identifies fatty acid metabolism members as potential predictive markers for cisplatin resistance
    Marc Warmoes
    OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
    Mol Cell Proteomics 12:1319-34. 2013
  6. pmc Differential detergent extraction of mycobacterium marinum cell envelope proteins identifies an extensively modified threonine-rich outer membrane protein with channel activity
    Aniek D van der Woude
    Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
    J Bacteriol 195:2050-9. 2013
  7. doi request reprint Composition of the type VII secretion system membrane complex
    Edith N G Houben
    Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
    Mol Microbiol 86:472-84. 2012
  8. doi request reprint Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling
    Meike de Wit
    Department of Pathology Tumor Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands Department of Medical Oncology OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands
    J Proteomics 99:26-39. 2014
  9. doi request reprint Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer
    Remond J A Fijneman
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Clin Cancer Res 18:2613-24. 2012
  10. pmc Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression
    Jakob Albrethsen
    OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center VUmc Cancer Center Amsterdam, The Netherlands
    Mol Cell Proteomics 9:988-1005. 2010

Collaborators

Detail Information

Publications20

  1. pmc Whole gel processing procedure for GeLC-MS/MS based proteomics
    Sander R Piersma
    Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands
    Proteome Sci 11:17. 2013
    ..Here we introduce the whole gel (WG) procedure where, prior to gel slice cutting, the processing steps are carried out on the whole gel...
  2. doi request reprint Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum
    Sander R Piersma
    OncoProteomics Laboratory, Department of Medical Oncology, VUMC Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
    J Proteome Res 9:1913-22. 2010
    ..Follow-up in serum of mice bearing MEF/Toff/IGF1R-induced tumors showed an increase of osteopontin levels paralleling tumor growth, and reduction in the serum of mice in which IGF1R expression was shut off and tumor regressed...
  3. ncbi request reprint Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues
    Jaco C Knol
    OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
    Biochim Biophys Acta 1844:1034-43. 2014
    ..Here, we examine biochemical tissue fractions containing chromatin-binding (CB) proteins in the context of colorectal cancer (CRC) progression...
  4. doi request reprint Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression
    Meike de Wit
    Department of Pathology Tumor Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands
    Gut 61:855-64. 2012
    ..The authors aimed to identify cell surface protein biomarkers with extracellular domains that could be targeted for molecular imaging and discriminate low-risk adenomas and normal colon from high-risk adenomas and CRC...
  5. pmc Proteomics of genetically engineered mouse mammary tumors identifies fatty acid metabolism members as potential predictive markers for cisplatin resistance
    Marc Warmoes
    OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
    Mol Cell Proteomics 12:1319-34. 2013
    ..Our data suggest that exploring the functional link between the DNA damage response and cancer metabolism shortly after the initial treatment may be a useful strategy to predict the efficacy of cisplatin...
  6. pmc Differential detergent extraction of mycobacterium marinum cell envelope proteins identifies an extensively modified threonine-rich outer membrane protein with channel activity
    Aniek D van der Woude
    Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
    J Bacteriol 195:2050-9. 2013
    ..The most surprising feature of MMAR_0617 is a long C-terminal threonine-rich domain with extensive modifications. In summary, we have identified a novel mycobacterial outer membrane porin with unusual properties...
  7. doi request reprint Composition of the type VII secretion system membrane complex
    Edith N G Houben
    Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
    Mol Microbiol 86:472-84. 2012
    ..These are the first data on a T7S membrane complex and, given the high conservation of its components, our data can likely be generalized to most mycobacterial T7S systems...
  8. doi request reprint Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling
    Meike de Wit
    Department of Pathology Tumor Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands Department of Medical Oncology OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands
    J Proteomics 99:26-39. 2014
    ..Further dedicated validation studies are required to demonstrate their clinical applicability...
  9. doi request reprint Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer
    Remond J A Fijneman
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Clin Cancer Res 18:2613-24. 2012
    ..Early detection of colorectal cancer (CRC) and its precursor lesions is an effective approach to reduce CRC mortality rates. This study aimed to identify novel protein biomarkers for the early diagnosis of CRC...
  10. pmc Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression
    Jakob Albrethsen
    OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center VUmc Cancer Center Amsterdam, The Netherlands
    Mol Cell Proteomics 9:988-1005. 2010
    ..Together, the results show that subnuclear proteomics of tumor tissue is feasible and a promising avenue for exploring oncogenesis...
  11. pmc Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer
    Marc Warmoes
    OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
    Mol Cell Proteomics 11:M111.013334. 2012
    ....
  12. ncbi request reprint Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector
    Aniek D van der Woude
    Department of Medical Microbiology and Infection Control, VU University Medical Center, Van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands Department of Molecular Microbiology, Institute of Molecular Cell Biology, VU University, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
    Cell Microbiol 16:280-95. 2014
    ..These results suggest that SecA2-dependent membrane localization of PknG is an important determinant for M. marinum virulence. ..
  13. doi request reprint Label-free mass spectrometry-based proteomics for biomarker discovery and validation
    Thang V Pham
    OncoProteomics Laboratory, CCA 1 60, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
    Expert Rev Mol Diagn 12:343-59. 2012
    ....
  14. doi request reprint On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics
    Thang V Pham
    OncoProteomics Laboratory, Department Medical Oncology, VUMC Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
    Bioinformatics 26:363-9. 2010
    ..A shortcoming of these tests is that they do not take into account within- and between-sample variations together. Hence, our aim is to improve upon existing techniques by incorporating both the within- and between-sample variations...
  15. doi request reprint Comparison of the performance of two affinity depletion spin filters for quantitative proteomics of CSF: Evaluation of sensitivity and reproducibility of CSF analysis using GeLC-MS/MS and spectral counting
    Silvina A Fratantoni
    OncoProteomics Laboratory, Department of Medical Oncology, VUMC Cancer Center Amsterdam, VU University Medical Center, The Netherlands
    Proteomics Clin Appl 4:613-7. 2010
    ..Our goal was to create a reproducible discovery workflow with acceptable throughput that can identify 500-1000 CSF proteins in small volumes of CSF...
  16. ncbi request reprint Strategies for kinome profiling in cancer and potential clinical applications: chemical proteomics and array-based methods
    Sander R Piersma
    Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
    Anal Bioanal Chem 397:3163-71. 2010
    ....
  17. ncbi request reprint Proteomic analysis of cerebrospinal fluid extracellular vesicles: A comprehensive dataset
    Davide Chiasserini
    OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
    J Proteomics 106:191-204. 2014
    ..Delineating the protein composition of extracellular vesicles in CSF is a first and crucial step to comprehend their origin and their function in the central nervous system and to establish their biomarker potential. ..
  18. pmc Specific chaperones for the type VII protein secretion pathway
    Maria H Daleke
    Department of Medical Microbiology and Infection Control, VU University Medical Center, 1081 BT Amsterdam, The Netherlands
    J Biol Chem 287:31939-47. 2012
    ..In conclusion, our study shows that EspG(5) and EspG(1) interact specifically with PE/PPE proteins that are secreted via their own ESX systems and suggests that EspG proteins are specific chaperones for the type VII pathway...
  19. pmc Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1-secreted proteins
    Musa Sani
    Division of Cell Biology B6, Netherlands Cancer Institute Antoni van Leeuwenhoek Hospital NKI AVL, Amsterdam, The Netherlands
    PLoS Pathog 6:e1000794. 2010
    ..Together, these results show a direct visualization of the mycobacterial capsular layer as a labile structure that contains ESX-1-secreted proteins...
  20. doi request reprint Proteomics of the TRAP-induced platelet releasate
    Sander R Piersma
    OncoProteomics Laboratory, Dept of Medical Oncology, VUMC Cancer Center Amsterdam, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
    J Proteomics 72:91-109. 2009
    ..This approach offers unique possibilities to analyse the role of platelet-secreted proteins in physiology and in diseases such as atherosclerosis and cancer...