GPMDB00473OtherBendz M, et al.InstrumentNot AvailableNot availableEscherichia_coli_k_12_substr__mg1655, Enterobacteria_phage_13a, Enterobacteria_phage_933w, Enterobacteria_phage_alpha3, Enterobacteria_phage_ba14, Enterobacteria_phage_bp_4795, Enterobacteria_phage_bz13, Enterobacteria_phage_cdti, Enterobacteria_phage_ecods1, Enterobacteria_phage_eps7, Enterobacteria_phage_epsilon15, Enterobacteria_phage_es18, Enterobacteria_phage_felix_01, Enterobacteria_phage_fels_2, Enterobacteria_phage_fi_sensu_lato, Enterobacteria_phage_g4_sensu_lato, Enterobacteria_phage_hk022, Enterobacteria_phage_hk620, Enterobacteria_phage_hk97, Enterobacteria_phage_i2_2, Enterobacteria_phage_id18_sensu_lato, Enterobacteria_phage_id2, Enterobacteria_phage_if1, Enterobacteria_phage_ike, Enterobacteria_phage_jk06, Enterobacteria_phage_js10, Enterobacteria_phage_js98, Enterobacteria_phage_jse, Enterobacteria_phage_k1e, Enterobacteria_phage_k1f, Enterobacteria_phage_k1_5, Enterobacteria_phage_lambda, Enterobacteria_phage_m13, Enterobacteria_phage_min27, Enterobacteria_phage_ms2, Enterobacteria_phage_mu, Enterobacteria_phage_n15, Enterobacteria_phage_n4, Enterobacteria_phage_p1, Enterobacteria_phage_p2, Enterobacteria_phage_p22, Enterobacteria_phage_p4, Enterobacteria_phage_phi1, Enterobacteria_phage_phieco32, Enterobacteria_phage_phiecom_gj1, Enterobacteria_phage_phip27, Enterobacteria_phage_phiv10, Enterobacteria_phage_phix174_sensu_lato, Enterobacteria_phage_prd1, Enterobacteria_phage_psp3, Enterobacteria_phage_rb14, Enterobacteria_phage_rb32, Enterobacteria_phage_rb43, Enterobacteria_phage_rb49, Enterobacteria_phage_rb51, Enterobacteria_phage_rb69, Enterobacteria_phage_rtp, Enterobacteria_phage_sf6, Enterobacteria_phage_sfv, Enterobacteria_phage_sp6, Enterobacteria_phage_ssl_2009a, Enterobacteria_phage_st104, Enterobacteria_phage_st64t, Enterobacteria_phage_st_1, Enterobacteria_phage_t1, Enterobacteria_phage_t3, Enterobacteria_phage_t4, Enterobacteria_phage_t5, Enterobacteria_phage_t7, Enterobacteria_phage_tls, Enterobacteria_phage_vt2_sakai, Enterobacteria_phage_wa13_sensu_lato, Enterobacteria_phage_wv8, Enterobacteria_phage_yyz_2008, Enterobacteriophage_qbetaarne@bioinfo.se23512833Science for Life Laboratory, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm Universityhttp://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015431http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015432http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015433http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015434http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015435http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015436http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015438Not availableGPMDBTopology analysis of membrane proteins can be obtained by enzymatic shaving in combination with MS identification of peptides. Ideally, such analysis could provide quite detailed information about the membrane spanning regions. Here, we examine the ability of some shaving enzymes to provide large-scale analysis of membrane proteome topologies. To compare different shaving enzymes, we first analyzed the detected peptides from two over-expressed proteins. Second, we analyzed the peptides from non-over-expressed Escherichia coli membrane proteins with known structure to evaluate the shaving methods. Finally, the identified peptides were used to test the accuracy of a number of topology predictors. At the end we suggest that the usage of thermolysin, an enzyme working at the natural pH of the cell for membrane shaving, is superior because: (i) we detect a similar number of peptides and proteins using thermolysin and trypsin; (ii) thermolysin shaving can be run at a natural pH and (iii) the incubation time is quite short. (iv) Fewer detected peptides from thermolysin shaving originate from the transmembrane regions. Using thermolysin shaving we can also provide a clear separation between the best and the less accurate topology predictors, indicating that using data from shaving can provide valuable information when developing new topology predictors.Membrane protein shaving with thermolysin can be used to evaluate topology predictors.Bendz Maria M,Skwark Marcin M,Nilsson Daniel D,Granholm Viktor V,Cristobal Susana S,Käll Lukas L,Elofsson Arne A,Bendz Maria M, Skwark Marcin M, Nilsson Daniel D, Granholm Viktor V, Cristobal Susana S, Käll Lukas L, Elofsson Arne Apolypeptide, Bacillus thermoproteolyticus neutral proteinase, membrane, membrane of organ, proteins, membranous organ component, Thermolysin S.AW488255, big, Integral Membrane Proteins, scale tissue, Procedures, determination, conformation, Biocatalysts, peltate hair, Surface Proteins, number, D430049E23Rik, Gene, bacterium E3, Membrane-Associated Proteins, Integral, electronic data file, Polypeptides, large, Hek6, Method, Escherchia coli, Gene Products, Studies, Cek6, Enteroinvasive Escherichia coli, Enterococcus coli, ENSMUSG00000074119, MAR, Cell Membrane, ERP, Erp, Elkh, Escherichia/Shigella coli, enzymes, plant peltate hair, Surface, EK6, Tyrosine-protein kinase receptor EPH-2, E coli, proteins, procedures, Sap-2, number of, E. coli, Eschericia coli, Enteroaggregative Escherichia coli, Study, 2.7.10.1, Solute carrier family 6 member 2, Methodological Studies, Etrp, great, has or lacks parts of type, SLC6A5, NET1, Membrane Associated Proteins, NAT1, Membrane Protein, relational structural quality, NET, Net, Alkalescens-Dispar Group, membrane, data, ELK, Elk, Bacterium coli, C130099E04Rik, IRF-1, Neuronally-expressed EPH-related tyrosine kinase, Proteins, EPH tyrosine kinase 2, Cell Surface, SAP2, enzyme activity, 9330129L11, extra or missing physical or functional parts, EAggEC, membranous organ component, Procedure, Enteroaggregative E. coli, mereological quality, polypeptide, Norepinephrine transporter, Diffusely Adherent E. coli, Bacillus coli, chemical analysis, Protein, Membrane Proteins, computer data file, EPH-like kinase 6, techniques, scales, Cell Surface Proteins, Diffusely Adherent Escherichia coli, membrane of organ, scale, Enteroinvasive E. coli, Membrane-Associated, expanded, Cell Membrane Proteins, Methodological, hEK6, Membrane, Methodological Study, cardinality., Protein Gene Products, Gene Proteins, Integral Membrane Protein, Bacterium coli commune, enlarged, EPHT2, assay, Proteomes, Integral Membrane, methodologypolypeptide, Bacillus thermoproteolyticus neutral proteinase, membrane, membrane of organ, proteins, membranous organ component, Thermolysin S.Integral Membrane Proteins, big, scale tissue, Procedures, determination, conformation, Effects, Biocatalysts, peltate hair, Surface Proteins, number, Gene, bacterium E3, Membrane-Associated Proteins, Integral, Long Term, period, Polypeptides, large, Method, Escherchia coli, Gene Products, Studies, ARB, Enteroinvasive Escherichia coli, Enterococcus coli, CD105, Effect, Cell Membrane, Escherichia/Shigella coli, enzymes, Identification, Longterm, cell, VMD2, plant peltate hair, Surface, beta-Trypsin, Bacillus thermoproteolyticus neutral proteinase, stubby, E coli, proteins, procedures, number of, Long-Term, BMD, cell surface MJ7/18 antigen, E. coli, Eschericia coli, Enteroaggregative Escherichia coli, Study, Thermolysin S, fully spanning plasma membrane, Methodological Studies, data., great, has or lacks parts of type, Membrane Associated Proteins, s, Long-Term Effect, Membrane Protein, relational structural quality, Long-Term Effects, HHT1, RP50, Alkalescens-Dispar Group, membrane, Bacterium coli, Edg, Proteins, Longterm Effect, integral to membrane, Cell Surface, enzyme activity, extra or missing physical or functional parts, EAggEC, membranous organ component, Procedure, Enteroaggregative E. coli, Cell, mereological quality, polypeptide, shortened, Diffusely Adherent E. coli, Bacillus coli, chemical analysis, Protein, Long Term Effects, Membrane Proteins, techniques, scales, END, TU15B, Cell Surface Proteins, ENG, Diffusely Adherent Escherichia coli, transmembrane, membrane of organ, scale, Enteroinvasive E. coli, Membrane-Associated, expanded, Tripcellim, Identifications (Psychology), Cell Membrane Proteins, Methodological, Membrane, Methodological Study, beta Trypsin, Longterm Effects, Protein Gene Products, Gene Proteins, Trypure, Integral Membrane Protein, Bacterium coli commune, clear, enlarged, cardinality, assay, ORW1, short, Proteomes, time, BEST, Integral Membrane, methodology4703http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015438dbgap_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~0human_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~0varsite~00.00.00.0144972239358420720.001.0falseMembrane protein shaving with thermolysin can be used to evaluate topology predictorsData from PASSEL: [[https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?datasetPassword=YV8455s&identifier=PASS00193 PASS00193]]. Data file: 110512_MB_LepB_65_10.mzXML. Published as part of Proteomics. 2013 Mar 20 . From the Abstract: {{i}}... Here, we examine the ability of some shaving enzymes to provide large-scale analysis of membrane proteome topologies. To compare different shaving enzymes, we first analyzed the detected peptides from two over-expressed proteins. Secondly, we analyzed the peptides from non over-expressed Escherichia coli membrane proteins with known structure to evaluate the shaving methods. Finally, the identified peptides were used to test the accuracy of a number of topology predictors ...{{/i}}2013-04-18GPM1121001543823512833