PXD009991 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Micro-scale RPLC-CZE-MS/MS for deep and highly sensitive bottom-up proteomics |
Description | Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has been well recognized for bottom-up proteomics. It has approached 4000-8000 protein identifications (IDs) from a human cell line, mouse brains or Xenopus embryos via coupling with liquid chromatography (LC) prefractionation. However, at least five hundred micrograms of complex proteome digests were required for the LC-CZE-MS/MS studies. This requirement of a large amount of initial peptide material impedes the application of CZE-MS/MS for deep bottom-up proteomics of mass-limited samples. In this work, we coupled micro-scale reversed-phase LC (µRPLC) based peptide prefractionation to dynamic pH junction based CZE-MS/MS for deep bottom-up proteomics of the MCF7 breast cancer cell proteome starting with only 5-µg peptides. The dynamic pH junction based CZE enabled a 500-nL sample injection from as low as a 1.5-µL peptide sample, using up to 33% of the available peptide material for an analysis. Two kinds of µRPLC prefractionation were investigated, C18 ZipTip and nanoflow RPLC. C18 ZipTip-CZE-MS/MS identified 4453 proteins from 5 µg of the MCF7 proteome digest and showed good qualitative and quantitative reproducibility. Nanoflow RPLC-CZE-MS/MS produced over 7500 protein IDs and nearly 60000 peptide IDs from the 5-µg MCF7 proteome digest. The nanoflow RPLC-CZE-MS/MS platform reduced the required amount of complex proteome digests for LC-CZE-MS/MS-based deep bottom-up proteomics by two orders of magnitude. Our work provides the proteomicscommunity with a powerful tool for deep and highly sensitive proteomics. |
HostingRepository | PRIDE |
AnnounceDate | 2018-08-16 |
AnnouncementXML | Submission_2018-08-16_08:33:26.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Liangliang Sun |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-06-01 01:43:24 | ID requested | |
⏵ 1 | 2018-08-16 08:33:27 | announced | |
Publication List
Yang Z, Shen X, Chen D, Sun L, Microscale Reversed-Phase Liquid Chromatography/Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Deep and Highly Sensitive Bottom-Up Proteomics: Identification of 7500 Proteins with Five Micrograms of an MCF7 Proteome Digest. Anal Chem, 90(17):10479-10486(2018) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: Micro-scale RPLC, CZE-MS/MS |
Contact List
Liangliang Sun |
contact affiliation | Michigan State University |
contact email | lsun@chemistry.msu.edu |
lab head | |
Liangliang Sun |
contact affiliation | Michigan State University |
contact email | lsun@chemistry.msu.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD009991
- Label: PRIDE project
- Name: Micro-scale RPLC-CZE-MS/MS for deep and highly sensitive bottom-up proteomics