PXD029115

PXD029115 is an original dataset announced via ProteomeXchange.

Title	Spatial proteomics reveals differences in the cellular architecture of antibody-producing CHO and plasma-cell derived cells
Description	Most of the recombinant biotherapeutics employed today to combat severe illnesses e.g. various types of cancer or autoimmune diseases are produced by Chinese hamster ovary (CHO) cells. To meet the growing demand of these pharmaceuticals, CHO cells are under constant development in order to enhance their stability and productivity. The last decades saw a shift from empirical cell line optimization towards rational cell engineering using a growing number of large omics datasets to alter cell physiology on various levels. Especially proteomics workflows reached new levels in proteome coverage and data quality due to advances in high-resolution mass spectrometry instrumentation. One type of workflow concentrates on spatial proteomics by usage of subcellular fractionation of organelles with subsequent shotgun mass spectrometry proteomics and machine learning algorithms to determine the subcellular localization of large portions of the cellular proteome at a given time. Here, we present the first subcellular spatial proteome of a CHO-K1 cell line producing high titers of recombinant antibody and comparison to the spatial proteome of an antibody-producing plasma cell-derived (PCD) myeloma cell line. Both cell lines show strong correlation of immunoglobulin G chains with chaperones and proteins associated in protein glycosylation within the endoplasmic reticulum compartment. However, we report differences in the localization of proteins associated to vesicle-mediated transport, transcription and translation, which may affect antibody production in both cell lines. Furthermore, pairing subcellular localization data with protein expression data revealed elevated protein masses for organelles in the secretory pathway in MPC-11 cells. Our study highlights the potential of subcellular spatial proteomics combined with protein expression as potent workflow to identify characteristics of highly efficient recombinant protein expressing cell lines.
HostingRepository	PRIDE
AnnounceDate	2022-08-02
AnnouncementXML	Submission_2022-08-02_08:27:24.796.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD029115
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Robin Kretz
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Cricetulus griseus; NCBI TaxID: 10029;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-13 22:39:26	ID requested
⏵ 1	2022-08-02 08:27:25	announced

Dataset with its publication pending

submitter keyword: Chinese hamster ovary, myeloma, subcellular proteomics, mass spectrometry, machine learning

Dieter Stoll
contact affiliation	University of Applied Sciences Albstadt-Sigmaringen, Department of Life Sciences, Anton-Günther-Straße 51, 72488 Sigmaringen, Germany
contact email	stoll@hs-albsig.de
lab head
Robin Kretz
contact affiliation	University of Applied Sciences Albstadt-Sigmaringen
contact email	Robin.Kretz@nmi.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD029115
     1. Label: PRIDE project
     2. Name: Spatial proteomics reveals differences in the cellular architecture of antibody-producing CHO and plasma-cell derived cells