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PXD000426-1

PXD000426 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAsn3 mass accuracy jurkat proteome
DescriptionThe use of internal calibrants (the so called lock mass approach) provides much greater accuracy in mass spectrometry based proteomics. However, the polydimethylcyclosiloxane (PCM) peaks commonly used for this purpose are quite unreliable, leading to missing calibrant peaks in spectra and correspondingly lower mass measurement accuracy. Therefore, we here introduce a universally applicable and robust internal calibrant, the tripeptide Asn3. We show that Asn3 is a substantial improvement over PCM both in terms of consistent detection and resulting mass measurement accuracy. Asn3 is also very easy to adopt in the lab, as it requires only minor adjustments to the analytical setup. Data analysis: For mass measurement accuracy (MMA) calculations and comparisons, the following Mascot workflow was used. From the MS/MS data in each LC run, Mascot Generic Files were created using Distiller software (version 2.4.3.3, Matrix Science, London, UK, www.matrixscience.com/distiller.html). These peak lists were then searched with the Mascot search engine (Matrix Science) using the Mascot Daemon interface (version 2.4.0, Matrix Science). Spectra were searched against the Swiss-Prot database (version 13_04 of UniProtKB/Swiss-Prot protein database containing 20,232 sequence entries of human proteins) concatenated with its reversed sequence database. Variable modifications were set to pyro-glutamate formation of amino terminal glutamine and acetylation of the protein N-terminus, whereas fixed modifications only included oxidation of methionine. Mass tolerance on peptide ions was set to 10 ppm (with Mascot’s C13 option set to 1), and the mass tolerance on peptide fragment ions was set to 20 millimass units (mmu), except for the space-charge effect experiment(LMA5) where an extra search was done with a setting of 3 mmu. The peptide charge was set to 1+,2+,3+ and instrument setting was put on ESI-QUAD. Enzyme was set to trypsin allowing for one missed cleavage, and cleavage was allowed when arginine or lysine is followed by proline. Only peptides that were ranked one and scored above the threshold score, set at 99% confidence, were withheld. All data was processed and managed by ms_lims.
HostingRepositoryPRIDE
AnnounceDate2013-10-22
AnnouncementXMLSubmission_2013-10-22_11:21:58.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000426
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterAn Staes
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; deaminated residue; N-acetylated residue
Instrumentorbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-08-22 14:32:16ID requested
⏵ 12013-10-22 11:22:11announced
22014-07-28 00:44:53announcedUpdated project metadata.
32015-02-17 03:03:14announcedUpdated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: LC-MS/MS, human, mass accuracy, LTQ-Orbitrap Velos
Contact List
An Staes
contact affiliationMedical Protein Chemistry
contact emailan.staes@vib-ugent.be
Kris Gevaert
contact attributekris.gevaert@vib-ugent.be
contact affiliationVIB Department of Medical Protein Research, UGent Proteome Analysis and Bioinformatics Unit
contact emailkris.gevaert@vib-ugent.be
Full Dataset Link List
Dataset FTP location
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Repository Record List
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