PXD034255

PXD034255 is an original dataset announced via ProteomeXchange.

Title	Coupling high-field asymmetric ion mobility spectrometry with capillary electrophoresis-electrospray ionization-tandem mass spectrometry improves protein identifications in bottom-up proteomic analysis of low nanogram samples
Description	In this work, we pioneered the assessment of coupling high-field asymmetric waveform ion mobility spectrometry (FAIMS) with ultra-sensitive capillary electrophoresis hyphenated with tandem mass spectrometry (CE-MS/MS) to achieve deeper proteome coverage of low nanogram amounts of digested cell lysates. An internal stepping strategy using three or four compensation voltages (CVs) per analytical run with varied cycle times was tested to determine optimal FAIMS settings and MS parameters for the CE-FAIMS-MS/MS method. The optimized method applied to bottom-up proteomic analysis of 1 ng HeLa protein digest standard identified 1,314±30 proteins, 4,829±200 peptide groups, and 7,577±163 peptide spectrum matches (PSMs) corresponding to a 16%, 25%, and 22% increase, respectively, over CE-MS/MS alone, without FAIMS. Furthermore, the percentage of acquired MS/MS spectra that resulted in PSMs increased nearly 2-fold with CE-FAIMS-MS/MS. Our results also identified from 1 ng HeLa protein digest without any prior enrichment, 76±9 phosphopeptides, 18% of which were multiphosphorylated. These results represent a 46% increase in phosphopeptide identifications over the control experiments without FAIMS yielding 2.5-fold more multiphosphorylated peptides.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:53.196.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
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-01 11:17:35	ID requested
1	2023-05-10 09:18:53	announced
⏵ 2	2023-11-14 08:46:01	announced	2023-11-14: Updated project metadata.

Johnson KR, Gregu, š M, Ivanov AR, Coupling High-Field Asymmetric Ion Mobility Spectrometry with Capillary Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry Improves Protein Identifications in Bottom-Up Proteomic Analysis of Low Nanogram Samples. J Proteome Res, 21(10):2453-2461(2022) [pubmed]

submitter keyword: FAIMS, ultra-sensitive proteomics, tandem mass spectrometry, bottom-up proteomics, capillary electrophoresis,CE-MS/MS

Alexander R. Ivanov
contact affiliation	Northeastern University
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/2023/05/PXD034255

PRIDE project URI

• PRIDE
  1. PXD034255
     1. Label: PRIDE project
     2. Name: Coupling high-field asymmetric ion mobility spectrometry with capillary electrophoresis-electrospray ionization-tandem mass spectrometry improves protein identifications in bottom-up proteomic analysis of low nanogram samples