title: Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project.
abstract: A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of combining -omics for a comprehensive characterization of specific biological systems.
authors.affiliation: Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.|Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Paula
authors.initials: P
authors.lastname: Díez
authors.affiliation: Bioinformatics and Functional Genomics Research Group, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Conrad
authors.initials: C
authors.lastname: Droste
authors.affiliation: Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Rosa M
authors.initials: RM
authors.lastname: Dégano
authors.affiliation: Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: María
authors.initials: M
authors.lastname: González-Muñoz
authors.affiliation: Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Nieves
authors.initials: N
authors.lastname: Ibarrola
authors.affiliation: Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Martín
authors.initials: M
authors.lastname: Pérez-Andrés
authors.affiliation: Division of Hepatology and Gene Therapy, Proteomics and Bioinformatics Unit, Centre for Applied Medical Research (CIMA), University of Navarra , 31008 Pamplona, Spain.
authors.forename: Alba
authors.initials: A
authors.lastname: Garin-Muga
authors.affiliation: Division of Hepatology and Gene Therapy, Proteomics and Bioinformatics Unit, Centre for Applied Medical Research (CIMA), University of Navarra , 31008 Pamplona, Spain.
authors.forename: Víctor
authors.initials: V
authors.lastname: Segura
authors.affiliation: Clinical Protein Science and Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University , BMC D13, 221 84 Lund, Sweden.
authors.forename: Gyorgy
authors.initials: G
authors.lastname: Marko-Varga
authors.affiliation: Biodesign Institute, Arizona State University , 1001 South McAllister Avenue, Tempe, Arizona 85287, United States.
authors.forename: Joshua
authors.initials: J
authors.lastname: LaBaer
authors.affiliation: Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Alberto
authors.initials: A
authors.lastname: Orfao
authors.affiliation: Division of Hepatology and Gene Therapy, Proteomics and Bioinformatics Unit, Centre for Applied Medical Research (CIMA), University of Navarra , 31008 Pamplona, Spain.
authors.forename: Fernando J
authors.initials: FJ
authors.lastname: Corrales
authors.affiliation: Bioinformatics and Functional Genomics Research Group, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: De Las Rivas
authors.affiliation: Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.|Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Fuentes
mesh_terms: D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D002874:Chromosome Mapping; D004591:Electrophoresis, Polyacrylamide Gel; D006801:Humans; D016393:Lymphoma, B-Cell / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D040901:Proteomics; D053719:Tandem Mass Spectrometry; D059467:Transcriptome
keywords: C-HPP; lymphoma B-cell line; protein expression profile; subcellular fractionation; transcriptomics