PXD042999

PXD042999 is an original dataset announced via ProteomeXchange.

Title	A Fast Workflow for Identification and Quantification of Proteomes
Description	The 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.
HostingRepository	iProX
AnnounceDate	2014-03-27
AnnouncementXML	Submission_2023-06-14_21:40:23.346.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wanlin Liu
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-14 21:39:44	ID requested
⏵ 1	2023-06-14 21:40:24	announced

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]

submitter keyword: proteomics, mass spectrometry, proteome coverage

Jun Qin
contact affiliation	Beijing Proteome Research Center
contact email	jqin@bcm.edu
lab head
Wanlin Liu
contact affiliation	Beijing Proteome Research Center
contact email	wanlin_liu@126.com
dataset submitter

iProX dataset URI