PXD010288

PXD010288 is an original dataset announced via ProteomeXchange.

Title	Global proteome rearrangement screen in interphasic and mitotic HeLa CCL2 cell line by SEC-SWATH-MS
Description	It has become increasingly clear that biological functions depend not only on the identity and quantity, but also the correct interplay among the biomolecules that constitute the cell. Importantly, proteins as the key effectors in the cell dynamically organize into complexes. This study describes a workflow to interrogate the role of dynamic proteome organization in biological functions. Specifically, we here characterize the proteome of the HeLa CCL2 cell line in interphase and mitosis, including the measurement of the protein complex assembly state with the goal to screen for functional proteome rearrangement. We employ an optimized SEC-SWATH-MS workflow to profile protein elution along size exclusion chromatographic fractionations of mild proteome extracts. Largely maintaining the integrity of protein association into complexes, the method captures the proteomes contextual state via the measure of protein appearance at distinct molecular weight. Quantitatively accurate readout of polypeptide elution profiles is achieved by bottom-up DIA/SWATH mass spectrometry, facilitating sensitive detection of quantitatively context-re-wiring proteins. The study quantitatively profiles 5044 proteins across 390 SWATH-MS maps. Statistical analysis pinpoints several hundred proteins with significantly altered cellular context indicated by altered quantitative elution behavior across distinct apparent molecular weight ranges measured in SEC. The results are validated by the reconciliation of established cell biology such as CDK1 recruitment by cyclin B1 and the mitotic disassembly of nuclear pore complexes as presented in the accompanying manuscript. The high quality chromatographic data further delineate distinct cellular assemblies such as a novel mitotic intermediate of nuclear pore complex disassembly that was validated by orthogonal methods. The study sheds light on altered proteome state in the pivotal process of cell division at systems scale. In contrast to typical quantitative approaches to study the proteome, SEC-SWATH-MS captures the biophysical context state of proteins that is often associated with protein function. Thus, the data may well support the discovery and validation of novel aspects and effectors of modular proteome function along cell cycle progression. Our workflow and study build the capacity to investigate biological systems including their higher order organization on the level of proteins and in a systems-wide fashion which will help to elucidate how biochemical functions, responses and phenotypes are generated within a cell.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:38.709.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Moritz Heusel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-02 23:21:33	ID requested
1	2019-05-10 06:42:05	announced
⏵ 2	2023-11-14 08:49:39	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

curator keyword: Biomedical

submitter keyword: Human, protein-protein complexes, HeLa, Cell Cycle, SWATH-MS, SEC, Mitosis

Prof. Ruedi Aebersold
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Moritz Heusel
contact affiliation	Lund University
contact email	moritz.heusel@med.lu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD010288
     1. Label: PRIDE project
     2. Name: Global proteome rearrangement screen in interphasic and mitotic HeLa CCL2 cell line by SEC-SWATH-MS