PXD013658

PXD013658 is an original dataset announced via ProteomeXchange.

Title	Surpassing 10,000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy
Description	Comprehensive 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:54:31.056.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jan Muntel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-29 02:14:58	ID requested
1	2019-08-12 08:10:59	announced
⏵ 2	2024-10-22 04:54:31	announced	2024-10-22: Updated project metadata.

Muntel J, Gandhi T, Verbeke L, Bernhardt OM, Treiber T, Bruderer R, Reiter L, 000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy. Mol Omics, 15(5):348-360(2019) [pubmed]

10.1039/c9mo00082h;

submitter keyword: liquid chromatography, DIA, testis cancer,hybrid library

Lukas Reiter
contact affiliation	Biognosys AG
contact email	lukas.reiter@biognosys.com
lab head
Jan Muntel
contact affiliation	Biognosys AG
contact email	jan.muntel@biognosys.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013658

PRIDE project URI

• PRIDE
  1. PXD013658
     1. Label: PRIDE project
     2. Name: Surpassing 10,000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy