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PXD003002

PXD003002 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMorpheus Spectral Counter
DescriptionLabel-free quantitative mass spectrometry (MS) based on the Normalized Spectral Abundance Factor (NSAF) has emerged as a simple and reasonably robust method to determine the relative abundance of individual proteins within complex mixtures. Here, we describe Morpheus Spectral Counter (MSpC) as the first computational tool that directly calculates NSAF values from output obtained from Morpheus, a fast, open-source, peptide-MS/MS matching engine compatible with high-resolution mass instruments. NSAF has distinct advantages over other MS-based quantification methods, including a higher dynamic range as compared to isobaric tags, no requirement to align and re-extract MS1 peaks, and increased speed. MSpC features an easy to use graphic user interface that additionally calculates both distributed and unique NSAF values to permit analyses of both protein families and isoforms/proteoforms. MSpC determinations of protein concentration were linear over several orders of magnitude based on the analysis of several high-mass accuracy datasets either obtained from the Proteomics Identifications Repository or generated de novo with total cell extracts spiked with purified Arabidopsis 20S proteasomes. The MSpC software was developed in C# and is open sourced under a permissive license with the code made available at http://dcgemperline.github.io/Morpheus_SpC/.
HostingRepositoryPRIDE
AnnounceDate2016-02-24
AnnouncementXMLSubmission_2016-02-24_03:04:49.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterDavid C Gemperline
SpeciesList scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-10-02 07:05:45ID requested
12016-02-24 03:04:50announced
Publication List
Gemperline DC, Scalf M, Smith LM, Vierstra RD, Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine. Proteomics, 16(6):920-4(2016) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: Label-free quantification, proteomics, spectral count, LC-MS/MS, Morpheus, bioinformatics, software
Contact List
Richard D. Vierstra
contact affiliationDepartment of Biology, Washington University-St. Louis St. Louis, Missouri 63130 USA
contact emailrdvierstra@wustl.edu
lab head
David C Gemperline
contact affiliationUW Madison
contact emaildcgemperline@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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Repository Record List
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