PXD014392

PXD014392 is an original dataset announced via ProteomeXchange.

Title	An improved nanoflow RPLC-CZE-MS/MS system with high peak capacity and sensitivity for nanogram bottom-up proteomics
Description	Novel mass spectrometry (MS)-based proteomic tools with extremely high sensitivity and high peak capacity are required for comprehensive characterization of protein molecules in mass-limited proteome samples. We previously reported a nanoflow RPLC-CZE-MS/MS (nanoRPLC-CZE-MS/MS) system for deep bottom-up proteomics of low micrograms of human cell samples (Yang et al. Anal. Chem. 2018, 90, 10479-10486). In this work, we further improved the sensitivity of the nanoRPLC-CZE-MS/MS system drastically via employing bovine serum albumin (BSA) treated sample vials, improving the nanoRPLC fraction collection procedure, and using a shorter capillary for fast CZE separation. The improved nanoRPLC-CZE produced a high peak capacity of 8500 for peptide separation. The improved system identified 6500 proteins from a MCF7 proteome digest starting with only 500-ng peptides using a Q-Exactive HF mass spectrometer. The system actually consumed roughly 100-ng peptides. The improved system produced a comparable number of protein identifications (IDs) to our previous system with 10-fold less sample consumption. The improved system is also comparable to the two-dimensional (2D) nanoRPLC-MS/MS system developed by the Mann’s group regarding the number of protein IDs starting with 500-ng human cell proteome digests but with 4-fold lower sample consumption. We further coupled single spot solid phase sample preparation (SP3) method to the improved nanoRPLC-CZE-MS/MS for bottom-up proteomics of 5000 HEK293T cells, resulting in 3689 protein IDs with the consumption of a peptide amount that corresponded to only roughly 1000 cells. This work represents the first study of a small number of human cells using CZE-MS/MS.
HostingRepository	PRIDE
AnnounceDate	2019-10-23
AnnouncementXML	Submission_2019-10-25_03:57:02.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

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-26 01:31:56	ID requested
1	2019-10-23 07:16:56	announced
⏵ 2	2019-10-25 03:57:03	announced	2019-10-25: Updated publication reference for PubMed record(s): 31610113.

Yang Z, Shen X, Chen D, Sun L, Improved Nanoflow RPLC-CZE-MS/MS System with High Peak Capacity and Sensitivity for Nanogram Bottom-up Proteomics. J Proteome Res, 18(11):4046-4054(2019) [pubmed]

submitter keyword: nanoRPLC-CZE-MS/MS, bottom-up proteomics, nanograms, human cells

Liangliang Sun
contact affiliation	Michigan State University, Department of Chemistry
contact email	lsun@chemistry.msu.edu
lab head
Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.edu
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/2019/10/PXD014392

PRIDE project URI

• PRIDE
  1. PXD014392
     1. Label: PRIDE project
     2. Name: An improved nanoflow RPLC-CZE-MS/MS system with high peak capacity and sensitivity for nanogram bottom-up proteomics