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PXD013658 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSurpassing 10,000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy
DescriptionComprehensive proteome quantification is crucial for a better understanding of underlying mechanisms of diseases. Liquid chromatography mass spectrometry (LC-MS) has become the method of choice for comprehensive proteome quantification due to its power and versatility. Even though great advances have been made in recent years, full proteome coverage for complex samples remains challenging due to the high dynamic range of protein expression. Additionally, when studying diseases regulatory proteins, biomarkers or potential drug targets are often low abundant, such as for instance kinases and transcription factors. Here, we show that with improvements in chromatography and data analysis the single shot proteome coverage can go beyond 10,000 proteins in human tissue. In a testis cancer study, we quantified 11,200 proteins using data independent acquisition (DIA). This depth was achieved with a false discovery rate of 1% which was experimentally validated using a two species test. We introduce the concept of hybrid libraries which combine the strength of direct searching of DIA data as well as the use of large project-specific or published DDA data sets. Remarkably deep proteome coverage is possible using hybrid libraries without the additional burden of creating a project-specific library.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJan Muntel
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF-X
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-04-29 02:14:58ID requested
12019-08-12 08:10:59announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: hybrid library, DIA, liquid chromatography, testis cancer
Contact List
Lukas Reiter
contact affiliationBiognosys AG
contact emaillukas.reiter@biognosys.com
lab head
Jan Muntel
contact affiliationBiognosys AG
contact emailjan.muntel@biognosys.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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