Acknowledgments
Contributions: AF, FF, and FU conceived and designed the project.
MV and FF prepared and conducted the showcase experiment. AF
and FF analyzed the showcase example. AF, FF, FU, and CM wrote
the manuscript. BC, LG, MG, and RA supervised, reviewed, and
edited the manuscript. MG and RA provided funding and resources
to support the project. Fig. 1 was created with BioRender.com.
Declaration of Interests: The authors declare no conflict of interest.
References
1. Ganem B, Li YT, Henion JD (1991) Observation of noncovalent enzyme substrate and
enzyme product complexes by ion-spray massspectrometry. J Am Chem Soc 113
(20):7818–7819
2. Savitski MM et al (2014) Tracking cancer
drugs in living cells by thermal profiling of the
proteome. Science 346(6205):1255784
3. Rappsilber J et al (2000) A generic strategy to
analyze the spatial organization of multiprotein complexes by cross-linking and mass
spectrometry. Anal Chem 72(2):267–275
4. Zhang Z, Smith DL (1993) Determination of
amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 2(4):522–531
5. Feng Y et al (2014) Global analysis of protein
structural changes in complex proteomes. Nat
Biotechnol 32(10):1036–1044
6. Leitner A (2016) Cross-linking and other
structural proteomics techniques: how chemistry is enabling mass spectrometry applications
in structural biology. Chem Sci 7
(8):4792–4803
7. Gavin AC et al (2006) Proteome survey reveals
modularity of the yeast cell machinery. Nature
440(7084):631–636
8. Roux KJ et al (2012) A promiscuous biotin
ligase fusion protein identifies proximal and
interacting proteins in mammalian cells. J Cell
Biol 196(6):801–810
9. Porath J, Flodin P (1959) Gel filtration—
method for desalting and group separation.
Nature 183(4676):1657–1659
10. Ramani AK et al (2008) A map of human protein interactions derived from co-expression of
human mRNAs and their orthologs. Mol Syst
Biol 4:180
11. Wessels HJCT et al (2009) LC-MS/MS as an
alternative for SDS-PAGE in blue native analysis of protein complexes. Proteomics 9
(17):4221–4228
12. Andersen JS et al (2003) Proteomic characterization of the human centrosome by protein
correlation
profiling.
Nature
426
(6966):570–574
13. Glatter T et al (2009) An integrated workflow
for charting the human interaction proteome:
insights into the PP2A system. Mol Syst Biol
5:237
14. Hauri S et al (2016) A high-density map for
navigating the human Polycomb Complexome. Cell Rep 17(2):583–595
15. Hauri S et al (2013) Interaction proteome of
human hippo signaling: modular control of the
co-activator YAP1. Mol Syst Biol 9:713
16. Huttlin EL et al (2015) The BioPlex network: a
systematic exploration of the human Interactome. Cell 162(2):425–440
17. Choi H et al (2011) SAINT: probabilistic scoring of affinity purification-mass spectrometry
data. Nat Methods 8(1):70–73
18. Scott NE et al (2017) Interactome disassembly
during apoptosis occurs independent of caspase
cleavage. Mol Syst Biol 13(1):906
19. Havugimana PC et al (2012) A census of
human soluble protein complexes. Cell 150
(5):1068–1081
20. Heusel M et al (2019) Complex-centric proteome profiling by SEC-SWATH-MS. Mol Syst
Biol 15(1):e8438
21. Heusel M et al (2020) A global screen for
assembly state changes of the mitotic proteome
by
SEC-SWATH-MS.
Cell
Syst
10
(2):133–155.e6
22. Bache N et al (2018) A novel LC system
embeds Analytes in pre-formed gradients for
rapid, ultra-robust proteomics. Mol Cell Proteomics 17(11):2284–2296
23. Gillet LC et al (2012) Targeted data extraction
of the MS/MS spectra generated by dataindependent acquisition: a new concept for
consistent and accurate proteome analysis.
Mol Cell Proteomics 11(6):p. O111 016717
System-Wide Profiling of Protein Complexes Via Size Exclusion. . .
293
Contributions: AF, FF, and FU conceived and designed the project.
MV and FF prepared and conducted the showcase experiment. AF
and FF analyzed the showcase example. AF, FF, FU, and CM wrote
the manuscript. BC, LG, MG, and RA supervised, reviewed, and
edited the manuscript. MG and RA provided funding and resources
to support the project. Fig. 1 was created with BioRender.com.
Declaration of Interests: The authors declare no conflict of interest.
References
1. Ganem B, Li YT, Henion JD (1991) Observation of noncovalent enzyme substrate and
enzyme product complexes by ion-spray massspectrometry. J Am Chem Soc 113
(20):7818–7819
2. Savitski MM et al (2014) Tracking cancer
drugs in living cells by thermal profiling of the
proteome. Science 346(6205):1255784
3. Rappsilber J et al (2000) A generic strategy to
analyze the spatial organization of multiprotein complexes by cross-linking and mass
spectrometry. Anal Chem 72(2):267–275
4. Zhang Z, Smith DL (1993) Determination of
amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 2(4):522–531
5. Feng Y et al (2014) Global analysis of protein
structural changes in complex proteomes. Nat
Biotechnol 32(10):1036–1044
6. Leitner A (2016) Cross-linking and other
structural proteomics techniques: how chemistry is enabling mass spectrometry applications
in structural biology. Chem Sci 7
(8):4792–4803
7. Gavin AC et al (2006) Proteome survey reveals
modularity of the yeast cell machinery. Nature
440(7084):631–636
8. Roux KJ et al (2012) A promiscuous biotin
ligase fusion protein identifies proximal and
interacting proteins in mammalian cells. J Cell
Biol 196(6):801–810
9. Porath J, Flodin P (1959) Gel filtration—
method for desalting and group separation.
Nature 183(4676):1657–1659
10. Ramani AK et al (2008) A map of human protein interactions derived from co-expression of
human mRNAs and their orthologs. Mol Syst
Biol 4:180
11. Wessels HJCT et al (2009) LC-MS/MS as an
alternative for SDS-PAGE in blue native analysis of protein complexes. Proteomics 9
(17):4221–4228
12. Andersen JS et al (2003) Proteomic characterization of the human centrosome by protein
correlation
profiling.
Nature
426
(6966):570–574
13. Glatter T et al (2009) An integrated workflow
for charting the human interaction proteome:
insights into the PP2A system. Mol Syst Biol
5:237
14. Hauri S et al (2016) A high-density map for
navigating the human Polycomb Complexome. Cell Rep 17(2):583–595
15. Hauri S et al (2013) Interaction proteome of
human hippo signaling: modular control of the
co-activator YAP1. Mol Syst Biol 9:713
16. Huttlin EL et al (2015) The BioPlex network: a
systematic exploration of the human Interactome. Cell 162(2):425–440
17. Choi H et al (2011) SAINT: probabilistic scoring of affinity purification-mass spectrometry
data. Nat Methods 8(1):70–73
18. Scott NE et al (2017) Interactome disassembly
during apoptosis occurs independent of caspase
cleavage. Mol Syst Biol 13(1):906
19. Havugimana PC et al (2012) A census of
human soluble protein complexes. Cell 150
(5):1068–1081
20. Heusel M et al (2019) Complex-centric proteome profiling by SEC-SWATH-MS. Mol Syst
Biol 15(1):e8438
21. Heusel M et al (2020) A global screen for
assembly state changes of the mitotic proteome
by
SEC-SWATH-MS.
Cell
Syst
10
(2):133–155.e6
22. Bache N et al (2018) A novel LC system
embeds Analytes in pre-formed gradients for
rapid, ultra-robust proteomics. Mol Cell Proteomics 17(11):2284–2296
23. Gillet LC et al (2012) Targeted data extraction
of the MS/MS spectra generated by dataindependent acquisition: a new concept for
consistent and accurate proteome analysis.
Mol Cell Proteomics 11(6):p. O111 016717
System-Wide Profiling of Protein Complexes Via Size Exclusion. . .
293