Chromosome 5
1.1. Group composition
Participating country(ies): Netherlands, Belgium
Head: Péter Horvatovich
Members:
- Rainer Bischoff clinical proteomics, PTM analysis
- Péter Horvatovich (bioinformatics, LC-MS analysis)
- Peter Verhaert (top-down analysis, proteomics and LC-MS analysis)
1.2. Missing proteins
Protein evidence according to NeXtProt for Chromosome 5:
Protein evidence status in text format is available here.
1.3. Bioinformatics protocols
- We dispose of quantitative LC-MS(/MS) workflows, time alignment methods, singel stage MS quantification and identification approaches based on TTP and SpectraST.
1.4. Analytical protocols
- We dispose of 2D-LC-MS/MS platform including nanoLC and an Agilent 6510 qTOF mass spectrometer.
1.5. Biological projects
- Chromosome 5 consortium has COPD, asthma and lung cancer research project performed in the laboratory of Dirkje Postma.
1.6. Biomaterials
- We dispose several bronchial epithelial cell lines, from stem cell stage until differentiated healthy on cancerous bronchial epithelial cells. Dirkje Postma group dispose as well clinically well characterized human Bronchoalveolar lavage fluid and lung tissues samples obtained from healthy persons as well from patient suffering from asthma, COPD and lung cancer.
1.7. Data sets
- PXD010115 In Klont et al. "Quantification of the Soluble Receptor of Advanced Glycation End-Products (sRAGE) by LC-MS Without the Use of Affinity Enrichment", Talanta, 2019, 1043:45-51.
- PXD008493 In Klont et al "Assessment of sample preparation bias in mass spectrometry-based proteomics", Analytical Chemistry, 2018, 90(8):5405-5413.
1.8. Special expertise
- Henry Lam dispose of special expertise in creating spectral libraries and using them for MS/MS peptide identification.
- Manfred Wuhrer group disposes glycopeptide measurement method to determine exact sequence compositions of N-glycopeptides.
1.9. Major achievements
- Setup Wiki for C-HPP (13 January 2013).
- Poster at C-HPP poster session of HUPO 2013 (Yokohama, Japan): Chromosome-Centric Human Protein Project: Chromosome 5, Peter Horvatovich, Pei-Jing Pai, Henry Lam, Rainer Bischoff. Poster in pdf is available here.
- Oral presentation at Young Investigator session and poster at HUPO 2013 (Yokohama, Japan): Pei-Jing Pai, Yingwei Hu, Henry Lam, Site-Specific N-Linked Glycosylation Analysis by Nano-LC Tandem Mass Spectrometry Coupled with a Spectral Library Searching Approach, References: YI03-03 11:29-11:41 for oral presentation and POS-03-016 for poster presentation.
- Organizing a DTL focus meeting on "Data integration, standards and fair principles in proteomics" in Utrecht on August 29, 2016, Utrecht, The Netherlands. See program at DTL website and presentation on the C-HPP Wiki.
- PhP test page
- Publications in 2015
1.10. The neXt-MP50 challenge
Plans:
- Participation in IVTT cluster, which target the 50 missing proteins in chromosomes 5, 10, 15, 16, and 19 that has the highest probability for identification in COV318, PANC1, DFCI024, D341MED, ST486, KLE cell line determined using mRNA array expression.
- Close collaboration with chromosome 19 team in Moonshot project performing deep profiling of 4000 melanoma samples and sharing bioinformatics expertise. In this project missing proteins can be obtained from deep profiling of large number of primary and metastatic melanoma samples.
- European trasncan-2 project on ovarian cancer will allow to obtain primary and metastatic protein profiles on large number of ovarian cancer samples, where missing proteins is expected to be identified.
- Local project on proteogenomics profiling of human lung tissue in context of COPD. Human lung tissue is highly complex in term of cell types, which can be the source of multiple missing proteins.