PMID- 38532014
OWN - NLM
STAT- MEDLINE
DCOM- 20240415
LR  - 20240506
IS  - 1548-7105 (Electronic)
IS  - 1548-7091 (Print)
IS  - 1548-7091 (Linking)
VI  - 21
IP  - 4
DP  - 2024 Apr
TI  - DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein 
      complexes.
PG  - 635-647
LID - 10.1038/s41592-024-02211-y [doi]
AB  - Most proteins are organized in macromolecular assemblies, which represent key 
      functional units regulating and catalyzing most cellular processes. Affinity 
      purification of the protein of interest combined with liquid chromatography 
      coupled to tandem mass spectrometry (AP-MS) represents the method of choice to 
      identify interacting proteins. The composition of complex isoforms concurrently 
      present in the AP sample can, however, not be resolved from a single AP-MS 
      experiment but requires computational inference from multiple time- and 
      resource-intensive reciprocal AP-MS experiments. Here we introduce deep 
      interactome profiling by mass spectrometry (DIP-MS), which combines AP with 
      blue-native-PAGE separation, data-independent acquisition with mass spectrometry 
      and deep-learning-based signal processing to resolve complex isoforms sharing the 
      same bait protein in a single experiment. We applied DIP-MS to probe the 
      organization of the human prefoldin family of complexes, resolving distinct 
      prefoldin holo- and subcomplex variants, complex-complex interactions and complex 
      isoforms with new subunits that were experimentally validated. Our results 
      demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and 
      resolution.
CI  - (c) 2024. The Author(s).
FAU - Frommelt, Fabian
AU  - Frommelt F
AUID- ORCID: 0000-0003-3666-8005
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland. fabian.frommelt@hotmail.com.
FAU - Fossati, Andrea
AU  - Fossati A
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland.
AD  - Quantitative Biosciences Institute (QBI), University of California San Francisco, 
      San Francisco, CA, USA.
AD  - Department of Cellular and Molecular Pharmacology, University of California San 
      Francisco, San Francisco, CA, USA.
AD  - J. David Gladstone Institutes, San Francisco, CA, USA.
FAU - Uliana, Federico
AU  - Uliana F
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland.
AD  - Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, 
      Switzerland.
FAU - Wendt, Fabian
AU  - Wendt F
AUID- ORCID: 0000-0002-2501-536X
AD  - Department of Health Sciences and Technology (D-HEST), Institute of Translational 
      Medicine (ITM), ETH Zurich, Zurich, Switzerland.
FAU - Xue, Peng
AU  - Xue P
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland.
AD  - Guangzhou National Laboratory, Guang Zhou, China.
FAU - Heusel, Moritz
AU  - Heusel M
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland.
FAU - Wollscheid, Bernd
AU  - Wollscheid B
AUID- ORCID: 0000-0002-3923-1610
AD  - Department of Health Sciences and Technology (D-HEST), Institute of Translational 
      Medicine (ITM), ETH Zurich, Zurich, Switzerland.
FAU - Aebersold, Ruedi
AU  - Aebersold R
AUID- ORCID: 0000-0002-9576-3267
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland.
FAU - Ciuffa, Rodolfo
AU  - Ciuffa R
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland.
FAU - Gstaiger, Matthias
AU  - Gstaiger M
AUID- ORCID: 0000-0002-3245-3253
AD  - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 
      Zurich, Switzerland. matthias.gstaiger@imsb.biol.ethz.ch.
LA  - eng
GR  - 115766/Innovative Medicines Initiative (IMI)/
GR  - 875510/Innovative Medicines Initiative (IMI)/
PT  - Journal Article
DEP - 20240326
PL  - United States
TA  - Nat Methods
JT  - Nature methods
JID - 101215604
RN  - 0 (Proteome)
RN  - 0 (Protein Isoforms)
SB  - IM
MH  - Humans
MH  - *Proteomics/methods
MH  - Chromatography, Affinity
MH  - *Proteome/analysis
MH  - Tandem Mass Spectrometry
MH  - Protein Isoforms
PMC - PMC11009110
COIS- M.H. was an employee of EVOSEP. The remaining authors declare no competing 
      interests.
EDAT- 2024/03/27 06:43
MHDA- 2024/04/15 06:43
PMCR- 2024/03/26
CRDT- 2024/03/27 00:26
PHST- 2023/03/22 00:00 [received]
PHST- 2024/02/14 00:00 [accepted]
PHST- 2024/04/15 06:43 [medline]
PHST- 2024/03/27 06:43 [pubmed]
PHST- 2024/03/27 00:26 [entrez]
PHST- 2024/03/26 00:00 [pmc-release]
AID - 10.1038/s41592-024-02211-y [pii]
AID - 2211 [pii]
AID - 10.1038/s41592-024-02211-y [doi]
PST - ppublish
SO  - Nat Methods. 2024 Apr;21(4):635-647. doi: 10.1038/s41592-024-02211-y. Epub 2024 
      Mar 26.