PXD027226

PXD027226 is an original dataset announced via ProteomeXchange.

Title	Capillary electrophoresis coupled to electrospray ionization tandem mass spectrometry (CE-MS/MS) for ultra-sensitive proteomic analysis of limited sample
Description	In this work, we developed an ultra-sensitive CE-MS/MS method for bottom-up proteomics analysis of limited samples, down to sub-nanogram levels of total protein. Analysis of 880 pg and 88 pg of HeLa protein digest standard by CE-MS/MS yielded ~1,100±46 and ~160±59 proteins, respectively, demonstrating higher protein and peptide identifications than the current state-of-the-art CE-MS/MS-based proteomic analyses with similar amounts of sample. To demonstrate potential applications of our ultra-sensitive CE-MS/MS method for analysis of limited biological samples, we digested 500 and 1,000 HeLa cells using a miniaturized in-solution digestion workflow. From 1-, 5-, and 10-cell equivalents injected from the resulted digests, we identified 744±127, 1,139±24, and 1,271±6 proteins and 3,353±719, 5,709±513, and 8,527±114 peptide groups, respectively. Furthermore, we performed a comparative assessment of CE-MS/MS and two reversed-phased nano-liquid chromatography (RP-nLC-MS/MS) methods (monolithic and packed columns) for the analysis of a ~10 ng HeLa protein digest standard. Our results demonstrate complementarity in the protein-, and especially peptide-level identifications of the evaluated CE-MS- and RP-nLC-MS-based methods. The techniques were further assessed to detect post-translational modifications and highlight the strengths of the CE-MS/MS approach in identifying potentially important and biologically relevant modified peptides. With a migration window of ~60 min, CE-MS/MS identified ~2,000±53 proteins on average from a single injection of ~8.8 ng HeLa protein digest standard. Additionally, an average of 232±10 phosphopeptides and 377±14 N-terminal acetylated peptides were identified in CE-MS/MS analyses at this sample amount corresponding to 2- and 1.5-fold more identifications for each respective modification found by nLC-MS/MS methods.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_05:19:07.750.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kendall Johnson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-11 22:47:30	ID requested
⏵ 1	2022-02-17 05:19:08	announced

Johnson KR, Gregu, š M, Kostas JC, Ivanov AR, Capillary Electrophoresis Coupled to Electrospray Ionization Tandem Mass Spectrometry for Ultra-Sensitive Proteomic Analysis of Limited Samples. Anal Chem, 94(2):704-713(2022) [pubmed]

submitter keyword: CE-MS, capillary electrophoresis, RP-nLC-MS, ultra-sensitive proteomics, monolithic columns, ultra-low flow liquid phase separation

Alexander R. Ivanov
contact affiliation	Northeastern University, Barnett Institute of Chemical andBiological Analysis, Department of Chemistry and Chemical Biology
contact email	a.ivanov@northeastern.edu
lab head
Kendall Johnson
contact affiliation	Barnett Insititute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University
contact email	johnson.kend@northeastern.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/2022/02/PXD027226

PRIDE project URI

• PRIDE
  1. PXD027226
     1. Label: PRIDE project
     2. Name: Capillary electrophoresis coupled to electrospray ionization tandem mass spectrometry (CE-MS/MS) for ultra-sensitive proteomic analysis of limited sample