PXD042999
PXD042999 is an original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2023-06-14 21:39:44 | ID requested | |
⏵ 1 | 2023-06-14 21:40:24 | announced |
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 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 |
Full Dataset Link List
iProX dataset URI |