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PXD000254

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2014-07-25
  • AnnouncementXML: Submission_2014-07-25_01:10:53.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Hannes Hahne
  • Title: DMSO enhances electrospray response boosting sensitivity of proteomic experiments
  • Description: We report that low percentages of dimethylsulfoxide (DMSO) in liquid chromatography solvents lead to a strong enhancement of electrospray ionization of peptides, improving the sensitivity of protein identification in bottom up proteomics by up to tenfold. The method can be easily implemented on any LC-MS/MS system without modification to hardware or software and at no additional cost. Peptide and protein identification and quantification: Raw MS data were processed by MaxQuant (version 1.3.0.3) for peak detection and quantification [PMID:19029910]. MS/MS spectra were searched against the IPI human database (version 3.68; 87,061 sequences. supplemented with 262 common contaminants) using the Andromeda search engine [PMID:21254760] with the following search parameters: full tryptic specificity, up to two missed cleavage sites, carbamidomethylation of cysteine residues set as a fixed modification and N-terminal protein acetylation and methionine oxidation as well as serine, threonine and tyrosine phosphorylation (where applicable) as variable modifications. Mass spectra were recalibrated within MaxQuant (first search 20 p.p.m. precursor tolerance) and subsequently re-searched with a mass tolerance of 6 p.p.m. Fragment ion mass tolerance was set to 20 p.p.m. Search results were filtered to a maximum false discovery rate (FDR) of 0.01 for proteins and peptides and a minimum peptide length of at least 6 aa was required.
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
  • Instrument: LTQ Orbitrap; LTQ Orbitrap Velos; LTQ Orbitrap Elite

Dataset History

VersionDatetimeStatusChangeLog Entry
02013-05-14 01:25:41ID requested
12013-08-07 03:38:27announced
22013-08-29 02:42:42announcedAdd reference
12014-07-25 01:10:53announced

Publication List

  1. Hahne H, Pachl F, Ruprecht B, Maier SK, Klaeger S, Helm D, Médard G, Wilm M, Lemeer S, Kuster B, DMSO enhances electrospray response, boosting sensitivity of proteomic experiments. Nat Methods, 10(10):989-91(2013) [pubmed]

Keyword List

  1. submitter keyword: Liquid chromatography-tandem mass spectrometry, electrospray ionization, proteomics, dimethyl sulfoxide

Contact List

    Hannes Hahne
    • contact affiliation: TU Muenchen, Chair of Proteomics and Bioanalytics
    • contact email: hannes.hahne@tum.de
    • dataset submitter:

Full Dataset Link List

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  2. PRIDE project URI
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