GPMDB00255OtherLoroch S, et al.InstrumentNot AvailableNot availableMus_musculus_viruses, Mousesickmann@isas.de25619855http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310007030http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310007039http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310007017Leibniz-Institut fuer Analytische Wissenschaften-ISAS-e.V., DortmundNot availableGPMDBQuantitative proteomics and phosphoproteomics have become key disciplines in understanding cellular processes. Fundamental research can be done using cell culture providing researchers with virtually infinite sample amounts. In contrast, clinical, pre-clinical and biomedical research is often restricted to minute sample amounts and requires an efficient analysis with only micrograms of protein. To address this issue, we generated a highly sensitive workflow for combined LC-MS-based quantitative proteomics and phosphoproteomics by refining an ERLIC-based 2D phosphoproteomics workflow into an ERLIC-based 3D workflow covering the global proteome as well. The resulting 3D strategy was successfully used for an in-depth quantitative analysis of both, the proteome and the phosphoproteome of murine cytomegalovirus-infected mouse fibroblasts, a model system for host cell manipulation by a virus. In a 2-plex SILAC experiment with 150 μg of a tryptic digest per condition, the 3D strategy enabled the quantification of ~75% more proteins and even ~134% more peptides compared to the 2D strategy. Additionally, we could quantify ~50% more phosphoproteins by non-phosphorylated peptides, concurrently yielding insights into changes on the levels of protein expression and phosphorylation. Beside its sensitivity, our novel three-dimensional ERLIC-strategy has the potential for semi-automated sample processing rendering it a suitable future perspective for clinical, pre-clinical and biomedical research.Multidimensional electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedical research.Loroch Stefan S,Schommartz Tim T,Brune Wolfram W,Zahedi René Peiman RP,Sickmann Albert A,Loroch Stefan S, Schommartz Tim T, Brune Wolfram W, Zahedi René Peiman RP, Sickmann Albert Anumber, count in organism, assay, quantitative, count, Chromatographies, determination, presence, chemical analysis, Proteomes., presence or absence in organism3.4.22.-, Viridae, data, MPFD, determination, Laboratory, CFTD, Mus domesticus, ACTA, number, mouse, mini-ICE, CASP-14, presence, House Mouse, body system, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, viruses, count in organism, Workflows, Experiment, count, House, Mus, sensitive, chemical analysis, Mini-ICE, CFTD1, Virus, Mus musculus domesticus, system, Animal, Animal., connected anatomical system, Work Flow, Zoophaginae, Mice, viral-, Mus musculus, Animal Virus, anatomical systems, Caspase-14 subunit p10, Viruses, CFTDM, Swiss, mice, Swiss Mouse, House Mice, Swiss Mice, Caspase-14 subunit p19, NEM2, ASMA, NEM3, "mouse" EXACT common_name [], MICE, NEM1, Laboratory Mice, domesticus, organ system, "house mouse" EXACT genbank_common_name [], "Mus muscaris" RELATED misnomer [], Vira, "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling [], Animal Viruses, Mouse, assay, quantitative, house mouse, Proteomes, Laboratory Mouse, Work Flows, Fibroblast, presence or absence in organismInvestigative Medicine, count in organism, Experimental, count, Investigative, determination, Research, chemical analysis, Medical Research, Investigational Medicine, Medicine, number, assay, quantitative, Chromatographies, Experimental Medicine., Medical, Proteomes, presence, Investigational, presence or absence in organism, Biomedicalprojections, 3.4.22.-, Viridae, CPD photolyase activity, Activity, PhrB photolyase activity, determination, Laboratory, lamellae, Mus domesticus, number, Gene, mini-ICE, CASP-14, photoreactivating enzyme activity, Experimental Medicine., pigmented epithelium, presence, process of organ, House Mouse, body system, phosphorylation, deoxyribodipyrimidine photolyase activity, stratum pigmentosum retinae, Biomedical, protrusion, lamella, Polypeptides, Readability, Investigative, House, sensitive, Medical Research, Virus, Gene Products, Mus musculus domesticus, system, stratum pigmentosa retinae, Animal, Research Activity, outer pigmented layer of retina, Work Flow, Laboratory Research, epithelium, Medical, Mice, sensitivity, Priorities, Animal Virus, anatomical systems, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Viruses, Research, Swiss, pigmented retina, min, Swiss Mice, proteins, ridges, "mouse" EXACT common_name [], DNA cyclobutane dipyrimidine photolyase activity, "Mus muscaris" RELATED misnomer [], pigment epithelium of retina, Vira, papilla, sample, pigmented retina epithelium, Investigational Medicine, Medicine, Sensitivity, "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling [], Development and Research, Research Priority, house mouse, laminae, PRE, anatomical protrusion, anatomical process, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, Proteins, lamina, mouse, Phosphorylations, flanges, Research Priorities, pigmented retinal epithelium, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, polypeptide, viruses, Investigative Medicine, count in organism, stratum pigmentosum (retina), Workflows, Priority, Experimental, Experiment, count, retinal pigment, Mus, chemical analysis, Mini-ICE, Protein, shelf, Research Activities, deoxyribonucleic photolyase activity, dipyrimidine photolyase (photosensitive), connected anatomical system, Zoophaginae, retinal pigment layer, viral-, flange, Investigational, organ process, Research and Development, Mus musculus, RPE, Caspase-14 subunit p10, photolyase activity, retinal pigmented epithelium, mice, shelves, Experimental Medicine, Swiss Mouse, Specificity, House Mice, Caspase-14 subunit p19, Understanding, MICE, projection, retinal pigment epithelium, ridge, sample population, p. pigmentosa retinae, Laboratory Mice, domesticus, Activities, organ system, Protein Gene Products, "house mouse" EXACT genbank_common_name [], process, processes, Gene Proteins, phr A photolyase activity, DNA-photoreactivating enzyme, Specificity and Sensitivity, spine, processus, Animal Viruses, deoxyribonucleate pyrimidine dimer lyase (photosensitive), Mouse, assay, quantitative, Proteomes, Laboratory Mouse, Work Flows, Fibroblast, presence or absence in organism2505http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310007030dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.00771128932757557050.01.0falseMultidimensional electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedicalData from ProteomeXchange, PXD ID: PXD001241. Experiment: ERLIC-2 Rep2, file: folder summary. Published as part of Biochim Biophys Acta. 2015 S1570-9639(15)00017-5 . From the Abstract: {{i}} ... we generated a highly sensitive workflow for combined LC-MS-based quantitative proteomics and phosphoproteomics by refining an ERLIC-based 2D phosphoproteomics workflow into an ERLIC-based 3D workflow covering the global proteome as well. The resulting 3D strategy was successfully used for an in-depth quantitative analysis of both, the proteome and the phosphoproteome of murine cytomegalovirus-infected mouse fibroblasts, a model system for host cell manipulation by a virus ... {{/i}}2015-02-26GPM3231000703025619855PXD001241PXD001241