PXD028965-1

PXD028965 is an original dataset announced via ProteomeXchange.

Title	Getting more out of FLAG-Tag co-immunoprecipitation mass spectrometry experiments using FAIMS.
Description	Co-immunoprecipitation of proteins coupled to mass spectrometry is critical for the understanding of protein interaction networks. In instances where a suitable antibody is not available, it is common to graft synthetic tags onto target protein sequences and allowing the use of commercially available antibodies for affinity purification. A common approach is through FLAG-Tag co-immunoprecipitation. To allow the selective elution of protein complexes, competitive displacement using a large molar excess of the tag peptides is often carried out. Yet, this creates downstream challenges for the mass spectrometry analysis due to the presence of large quantities of these peptides. Here, we demonstrate that Field Asymmetric Ion Mobility Spectrometry (FAIMS), a gas phase ion separation device prior to mass spectrometry analysis can be applied to FLAG-Tag co-immunoprecipitation experiment to increase the depth of protein coverage. By excluding these abundant tag peptides, we were able to observe deeper coverage of interacting proteins and as a result, deeper biological insights, without the need for additional sample handling or altering sample preparation protocols.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:09:23.298.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ching-Seng Ang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-06 06:05:23	ID requested
⏵ 1	2024-10-08 11:09:24	announced

10.1016/j.jprot.2021.104473;

submitter keyword: FAIMS,Co-IP mass spectrometry, FLAG Tag, Proteomics, ion mobility

Nicholas A. Williamson
contact affiliation	Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3052, Australia
contact email	nawill@unimelb.edu.au
lab head
Ching-Seng Ang
contact affiliation	University of Melbourne
contact email	cang@unimelb.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028965
     1. Label: PRIDE project
     2. Name: Getting more out of FLAG-Tag co-immunoprecipitation mass spectrometry experiments using FAIMS.