GPMDB00516OtherKelstrup CD, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Human_femalechdake@cpr.ku.dk25349961NNF Center for Protein Research, University of Copenhagenhttp://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004811http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004812http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004815http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004804http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004805http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004813http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004802http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004814http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004803http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004808http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004809http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004806http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004807Not availableGPMDBShotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate the faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage is evaluated by four different acquisition methods and benchmarked across three generations of Q Exactive instruments (ProteomeXchange data set PXD001305). We find the ultra-high-field Orbitrap mass analyzer to be capable of attaining a sequencing speed above 20 Hz, and it routinely exceeds 10 peptide spectrum matches per second or up to 600 new peptides sequenced per gradient minute. We identify 4400 proteins from 1 μg of HeLa digest using a 1 h gradient, which is an approximately 30% improvement compared to that with previous instrumentation. In addition, we show that very deep proteome coverage can be achieved in less than 24 h of analysis time by offline high-pH reversed-phase peptide fractionation, from which we identify more than 140,000 unique peptide sequences. This is comparable to state-of-the-art multiday, multienzyme efforts. Finally, the acquisition methods are evaluated for single-shot phosphoproteomics, where we identify 7600 unique HeLa phosphopeptides in one gradient hour and find the quality of fragmentation spectra to be more important than quantity for accurate site assignment.Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer.Kelstrup Christian D CD,Jersie-Christensen Rosa R RR,Batth Tanveer S TS,Arrey Tabiwang N TN,Kuehn Andreas A,Kellmann Markus M,Olsen Jesper V JV,Kelstrup Christian D CD, Jersie-Christensen Rosa R RR, Batth Tanveer S TS, Arrey Tabiwang N TN, Kuehn Andreas A, Kellmann Markus M, Olsen Jesper V JVdeep, developmental field., field, organ field, future organ, ProteomesOCT, data, PlexA2, Glass, Meth, Procedures, PLXN2, developmental field, HeLa, 2810428A13Rik, analyzer, future organ, Methodological, procedures, Procedure, Chalk, Methodological Study, AA589422, Speed, Study, organ field, Experiment, AW457381, Methodological Studies, Ice, velocity, Method, Tina, Studies, RCB0007, field, techniques, methodology., Plxn2, Proteomes, mKIAA0463, Crystaldeep, developmental field., field, organ field, future organ, Proteomesapparatus, OG12X, trait., Meth, Procedures, Data Set, determination, Effects, Arts, Proteins, Longterm Effect, instruments, Gene, future organ, 9930121L06Rik, 6330543G17Rik, Procedure, backward, Chalk, Long Term, polypeptide, peptide, period, Polypeptides, organ field, devices, equipment, Method, chemical analysis, Protein, Long Term Effects, Tina, Gene Products, Studies, field, techniques, Effect, Crystal, AI661365, deep, Art, Industrial, appliances, Glass, Industrial Arts, Longterm, developmental field, HeLa, min, proteins, analyzer, Methodological, procedures, Long-Term, Methodological Study, SHOT, OG12, Longterm Effects, Protein Gene Products, Speed, Study, Gene Proteins, Methodological Studies, Snm1l, h, Ice, velocity, s, RCB0007, Long-Term Effect, assay, Og12x, Proteomes, Long-Term Effects, time, Prx3, methodology, reversed5106http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004807dbgap_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~3lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0157310302282541660.01.0falseRapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer.Data from ProteomeXchange, PXD ID: PXD001305. Experiment: UPLC9_RJC_DEV_HeLa_02, file: 20140418_QE7_UPLC9_RJC_DEV_HeLaFrac1_02.mzml. Published as part of J Proteome Res. 2014 Oct 28 . From the Abstract: {{i}} Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage is evaluated by four different acquisition methods and benchmarked across three generations of Q Exactive instruments ... {{/i}}2014-11-02GPM3232000480725349961PXD001305PXD001305