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PXD042999

PXD042999 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA Fast Workflow for Identification and Quantification of Proteomes
DescriptionThe current in-depth proteomics makes use of long chromatography gradient to get access to more peptides for protein identification, resulting in covering of as many as 8000 mammalian gene products in 3 days of mass spectrometer running time. Here we report a fast sequencing (Fast-seq) workflow of the use of dual reverse phase high performance liquid chromatography - mass spectrometry (HPLC-MS) with a short gradient to achieve the same proteome coverage in 0.5 day. We adapted this workflow to a quantitative version (Fast quantification, Fast-quan) that was compatible to large-scale protein quantification. We subjected two identical samples to the Fast-quan workflow, which allowed us to systematically evaluate different parameters that impact the sensitivity and accuracy of the workflow. Using the statistics of significant test, we unraveled the existence of substantial falsely quantified differential proteins and estimated correlation of false quantification rate and parameters that are applied in label-free quantification. We optimized the setting of parameters that may substantially minimize the rate of falsely quantified differential proteins, and further applied them on a real biological process. With improved efficiency and throughput, we expect that the Fast-seq/Fast-quan workflow, allowing pair wise comparison of two proteomes in 1 day may make MS available to the masses and impact biomedical research in a positive way.
HostingRepositoryiProX
AnnounceDate2014-03-27
AnnouncementXMLSubmission_2023-06-14_21:40:23.346.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterWanlin Liu
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-06-14 21:39:44ID requested
12023-06-14 21:40:24announced
Publication List
Ding C, Jiang J, Wei J, Liu W, Zhang W, Liu M, Fu T, Lu T, Song L, Ying W, Chang C, Zhang Y, Ma J, Wei L, Malovannaya A, Jia L, Zhen B, Wang Y, He F, Qian X, Qin J, A fast workflow for identification and quantification of proteomes. Mol Cell Proteomics, 12(8):2370-80(2013) [pubmed]
Keyword List
submitter keyword: proteomics, mass spectrometry, proteome coverage
Contact List
Jun Qin
contact affiliationBeijing Proteome Research Center
contact emailjqin@bcm.edu
lab head
Wanlin Liu
contact affiliationBeijing Proteome Research Center
contact emailwanlin_liu@126.com
dataset submitter
Full Dataset Link List
iProX dataset URI