GPMDB00205OtherShalit T, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Human_female, Escherichia_coli_k_12_substr__mg165525780947yishai.levin@weizmann.ac.ilhttp://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014335http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014336http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014337http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014338http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014339http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014340http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014341http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014342http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014343http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014344http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014334Weizmann Institute of ScienceNot availableGPMDBPresented is a data set for benchmarking MS1-based label-free quantitative proteomics using a quadrupole orbitrap mass spectrometer. Escherichia coli digest was spiked into a HeLa digest in four different concentrations, simulating protein expression differences in a background of an unchanged complex proteome. The data set provides a unique opportunity to evaluate the proteomic platform (instrumentation and software) in its ability to perform MS1-intensity-based label-free quantification. We show that the presented combination of informatics and instrumentation produces high precision and quantification accuracy. The data were also used to compare different quantitative protein inference methods such as iBAQ and Hi-N. The data can also be used as a resource for development and optimization of proteomics informatics tools, thus the raw data have been deposited to ProteomeXchange with identifier PXD001385.MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer.Shalit Tali T,Elinger Dalia D,Savidor Alon A,Gabashvili Alexandra A,Levin Yishai Y,Shalit Tali T, Elinger Dalia D, Savidor Alon A, Gabashvili Alexandra A, Levin Yishai Yfree., Striated muscle activator of Rho-dependent signaling, Stars, STARS, MS1, Ms1Alkalescens-Dispar Group, Applications Software, data, Bacterium coli, apparatus, Stars, Computer Software, Data Set, IRF-1, Health Care Benchmarking, free., number, instruments, bacterium E3, Benchmark, EAggEC, Computer, Healthcare Benchmarking, Enteroaggregative E. coli, presence, Software Tools, Tool, Programs, polypeptide, Program, Computer Applications, count in organism, devices, Software Tool, count, equipment, Ms1, Diffusely Adherent E. coli, Bacillus coli, Escherchia coli, Computer Applications Software, Computer Applications Softwares, Health Care, Enteroinvasive Escherichia coli, Software Engineering, Analysis, Enterococcus coli, background, Softwares, Software, Computer Program, Application, MAR, Diffusely Adherent Escherichia coli, appliances, Software Applications, Escherichia/Shigella coli, Enteroinvasive E. coli, MS1, Software Application, HeLa, Striated muscle activator of Rho-dependent signaling, Engineering, Computer Programs and Programming, E coli, proteins, free, E. coli, introduction, Computer Software Application, Eschericia coli, Enteroaggregative Escherichia coli, Computer Programs, Applications, Applications Softwares, Benchmarks, Bacterium coli commune, Tools, Benchmarking, Concentration, Best Practice Analysis, Concentrations, Best Practice, RCB0007, quantitative, Healthcare, STARS, Proteomes, Attentions, presence or absence in organism, Computer Software Applicationsfree., Striated muscle activator of Rho-dependent signaling, Stars, STARS, MS1, Ms1Bru, apparatus, Procedures, single-organism developmental process, Raw, Health Care Benchmarking, number, instruments, bacterium E3, Computer, Healthcare Benchmarking, presence, devices, Ms1, Method, Escherchia coli, Studies, Enteroinvasive Escherichia coli, Software Engineering, Del(8)44H, Analysis, Enterococcus coli, Computer Program, Application, Svc, appliances, Escherichia/Shigella coli, MS1, Software Application, HeLa, Computer Programs and Programming, E coli, proteins, procedures, free, E. coli, Computer Software Application, Eschericia coli, Enteroaggregative Escherichia coli, Study, Benchmarks, Tools, Methodological Studies, Benchmarking, Concentration, data., Concentrations, Best Practice, RCB0007, Healthcare, Alkalescens-Dispar Group, Applications Software, data, Bacterium coli, Stars, Computer Software, Data Set, Benchmark, EAggEC, Procedure, Enteroaggregative E. coli, Software Tools, Tool, Programs, polypeptide, development, Program, Computer Applications, count in organism, Software Tool, count, equipment, Diffusely Adherent E. coli, Bacillus coli, Computer Applications Software, Computer Applications Softwares, Health Care, background, Softwares, techniques, Software, Diffusely Adherent Escherichia coli, Software Applications, Col4a-1, Enteroinvasive E. coli, Striated muscle activator of Rho-dependent signaling, Engineering, Methodological, Methodological Study, introduction, Computer Programs, Applications, Applications Softwares, Bacterium coli commune, Best Practice Analysis, quantitative, STARS, Attentions, Proteomes, methodology, presence or absence in organism, Computer Software Applications2005http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014338dbgap_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 Reanalysis0.00.00.0061690314620604570.01.0falseMS1-Based Label-Free Proteomics Using a Quadrupole Orbitrap Mass Spectrometer.Data from ProteomeXchange, PXD ID: PXD001385. File: QEP1_SpikeIn_230914_3_3ng_270914.mzml. Published as part of J Proteome Res. 2015 Mar 24 . From the Abstract: {{i}} Presented is a data set for benchmarking MS1-based label-free quantitative proteomics using a quadrupole orbitrap mass spectrometer. Escherichia coli digest was spiked into a HeLa digest in four different concentrations, simulating protein expression differences in a background of an unchanged complex proteome. The data set provides a unique opportunity to evaluate the proteomic platform (instrumentation and software) in its ability to perform MS1-intensity-based label-free quantification. {{/i}}2015-03-26GPM3232001433825780947PXD001385PXD001385