PXD044393

PXD044393 is an original dataset announced via ProteomeXchange.

Title	Enhancing proteome coverage by using strong anion exchange in tandem with basic-pH reversed-phase chromatography for sample multiplexing-based proteomics
Description	Sample multiplexing-based proteomic strategies rely on fractionation to improve proteome coverage. Tandem mass tag (TMT) experiments, for example, can currently accommodate up to 18 samples with proteins spanning several orders of magnitude, thus necessitating fractionation to achieve reasonable proteome coverage. Here, we present a simple yet effective peptide fractionation strategy that partitions a pooled TMT sample with a two-step elution using a strong anion exchange (SAX) spin column prior to gradient-based basic pH reversed-phase (BPRP) fractionation. We highlight our strategy with a TMTpro18-plex experiment using nine diverse human cell lines in biological duplicate. We collected three datasets, one using only BPRP fractionation, and two others of each SAX-partition followed by BPRP. The three datasets quantified a similar number of proteins and peptides, and the data highlight noticeable differences in the distribution of peptide charge and isoelectric point between the SAX partitions. The combined SAX partition dataset contributed 10% more proteins and 20% more unique peptides that were not quantified by BPRP fractionation alone. In addition to this improved fractionation strategy, we provide an online resource of relative abundance profiles for over 11,000 proteins across the nine human cell lines investigated herein.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:19:02.361.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-05 15:43:18	ID requested
1	2023-12-28 12:02:59	announced
⏵ 2	2024-10-22 06:19:03	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.3c00492;

Zhang T, Liu X, Rossio V, Dawson SL, Gygi SP, Paulo JA, Enhancing Proteome Coverage by Using Strong Anion-Exchange in Tandem with Basic-pH Reversed-Phase Chromatography for Sample Multiplexing-Based Proteomics. J Proteome Res, 23(8):2870-2881(2024) [pubmed]

submitter keyword: FAIMS, TMTpro, Eclipse, SAX,SPS-MS3, RTS

Joao A. Paulo
contact affiliation	Harvard Medical School Department of Cell Biology Harvard Medical School Boston, MA, USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.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/2023/12/PXD044393

PRIDE project URI

• PRIDE
  1. PXD044393
     1. Label: PRIDE project
     2. Name: Enhancing proteome coverage by using strong anion exchange in tandem with basic-pH reversed-phase chromatography for sample multiplexing-based proteomics