PXD022721-1

PXD022721 is an original dataset announced via ProteomeXchange.

Title	: Robust and reproducible large-scale label-free deep quantitative profiling of the MOLM-14 surfaceome using three mass spectrometry platforms over multiple years
Description	Surface proteins are one of the most important and common matrices for clinical chemistry and proteomic analyses. With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. Here, we evaluate the performance of three mass spectrometers, namely Orbitrap Elite (Hybrid Ion Trap-Orbitrap), Q Exactive HF (Hybrid Quadrupole-Orbitrap) and Orbitrap Fusion (Tribrid Quadrupole-Ion Trap-Orbitrap), in label-free semiquantitative analysis of cell surface proteins spanning a four-year period. Sucrose gradient ultracentrifugation was used for surfaceome enrichment, following gel separation for in-depth protein identification. With the established workflow, we identify 2335 cell surface proteins in MOLM-14, a human acute myeloid leukemia cell line, with a high degree of reproducibility across three MS platforms over multiple years.
HostingRepository	PRIDE
AnnounceDate	2021-12-30
AnnouncementXML	Submission_2021-12-30_15:04:43.404.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Aplenc
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Orbitrap Fusion; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-25 03:23:06	ID requested
⏵ 1	2021-12-30 15:04:44	announced

Lu C, Glisovic-Aplenc T, Bernt KM, Nestler K, Cesare J, Cao L, Lee H, Fazelinia H, Chinwalla A, Xu Y, Shestova O, Xing Y, Gill S, Li M, Garcia B, Aplenc R, Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms. J Proteome Res, 20(11):5203-5211(2021) [pubmed]

submitter keyword: Surfaceome, Mass spectrometry, Label-free quantification, Quantitative proteomics, Large-scale, Reproducibility

Richard Aplenc
contact affiliation	Children's Hospital of Philadelphia
contact email	aplenc@chop.edu
lab head
Richard Aplenc
contact affiliation	Children's Hospital of Pennsylvania University of Pennsylvania
contact email	aplenc@chop.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/2021/12/PXD022721

PRIDE project URI

• PRIDE
  1. PXD022721
     1. Label: PRIDE project
     2. Name: : Robust and reproducible large-scale label-free deep quantitative profiling of the MOLM-14 surfaceome using three mass spectrometry platforms over multiple years