References
1. Rigaut G, Shevchenko A, Rutz B, Wilm M,
Mann M, Seraphin B (1999) A generic protein
purification method for protein complex characterization and proteome exploration. Nat
Biotechnol 17:1030–1032
2. Daulat AM, Maurice P, Jockers R (2009)
Recent methodological advances in the discovery of GPCR-associated protein complexes.
Trends Pharmacol Sci 30:72–78
3. Ivarsson Y (2012) Plasticity of PDZ domains in
ligand recognition and signaling. FEBS Lett
586:2638–2647
4. te Velthuis AJ, Sakalis PA, Fowler DA,
Bagowski CP (2011) Genome-wide analysis
of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PLoS One 6:e16047
5. Nonaka H, Takei K, Umikawa M, Oshiro M,
Kuninaka K, Bayarjargal M, Asato T,
Yamashiro Y, Uechi Y, Endo S, Suzuki T, Kariya KI (2008) MINK is a Rap2 effector for
phosphorylation of the postsynaptic scaffold
protein TANC1. Biochem Biophys Res Commun 377:573–578
6. Han S, Nam J, Li Y, Kim S, Cho SH, Cho YS,
Choi SY, Choi J, Han K, Kim Y, Na M, Kim H,
Bae YC, Kim E (2010) Regulation of dendritic
spines, spatial memory, and embryonic development by the TANC family of PSD-95-interacting proteins. J Neurosci 30:15102–15112
7. Rabilloud T (1999) Silver staining of 2-D electrophoresis gels. Methods Mol Biol
112:297–305
8. Smaczniak C, Li N, Boeren S, America T, van
Dongen W, Goerdayal SS, de Vries S, Angenent GC, Kaufmann K (2012) Proteomicsbased identification of low-abundance signaling and regulatory protein complexes in native
plant tissues. Nat Protoc 7:2144–2158
9. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass
spectrometry-based shotgun proteomics. Nat
Protoc 11:2301–2319
10. Tyanova S, Temu T, Sinitcyn P, Carlson A,
Hein MY, Geiger T, Mann M, Cox J (2016)
The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat
Methods 13:731–740
11. Tyanova S, Cox J (2018) Perseus: a bioinformatics platform for integrative analysis of proteomics data in cancer research. Methods Mol
Biol 1711:133–148
12. Bouyssie ´ D, Hesse AM, Mouton-Barbosa E,
Rompais M, Macron C, Carapito C, de Peredo
AG, Coute ´ Y, Dupierris V, Burel A, Menetrey
JP, Kalaitzakis A, Poisat J, Romdhani A, BurletSchiltz O, Cianfe ´rani S, Garin J, Bruley C
(2020) Proline: an efficient and user-friendly
software suite for large-scale proteomics. Bioinformatics 36(10):3148–3155
13. Daulat AM, Puvirajesinghe TM, Camoin L,
Borg JP (2018) Mapping cellular polarity networks using mass spectrometry-based strategies. J Mol Biol 430:3545–3564
14. Cartier-Michaud A, Bailly AL, Betzi S, Shi X,
Lissitzky JC, Zarubica A, Serge A, Roche P,
Lugari A, Hamon V, Bardin F, Derviaux C,
Lembo F, Audebert S, Marchetto S,
Durand B, Borg JP, Shi N, Morelli X,
Aurrand-Lions M (2017) Genetic, structural,
and chemical insights into the dual function of
GRASP55 in germ cell Golgi remodeling and
JAM-C polarized localization during spermatogenesis. PLoS Genet 13:e1006803
15. Gagnoux-Palacios L, Awina H, Audebert S,
Rossin A, Mondin M, Borgese F, Planas-BoteyC, Mettouchi A, Borg JP, Hueber AO (2018)
Cell polarity and adherens junction formation
inhibit epithelial Fas cell death receptor signaling. J Cell Biol 217:3839–3852
16. Ernkvist M, Luna Persson N, Audebert S,
Lecine P, Sinha I, Liu M, Schlueter M,
Horowitz A, Aase K, Weide T, Borg JP,
Majumdar A, Holmgren L (2009) The
Amot/Patj/Syx signaling complex spatially
controls RhoA GTPase activity in migrating
endothelial cells. Blood 113:244–253
17. Belotti E, Polanowska J, Daulat AM,
Audebert S, Thome V, Lissitzky JC, Lembo F,
Blibek K, Omi S, Lenfant N, Gangar A,
Montcouquiol M, Santoni MJ, Sebbagh M,
Aurrand-Lions M, Angers S, Kodjabachian L,
Reboul J, Borg JP (2013) The human
PDZome: a gateway to PSD95-Disc
large-zonula occludens (PDZ)-mediated functions. Mol Cell Proteomics 12:2587–2603
18. Mojallal M, Zheng Y, Hultin S, Audebert S,
van Harn T, Johnsson P, Lenander C, Fritz N,
Mieth C, Corcoran M, Lembo F, Hallstrom M,
Hartman J, Mazure NM, Weide T, Grander D,
Borg JP, Uhlen P, Holmgren L (2014)
AmotL2 disrupts apical-basal cell polarity and
promotes tumour invasion. Nat Commun
5:4557
19. Bai Y, Markham K, Chen F, Weerasekera R,
Watts J, Horne P, Wakutani Y, Bagshaw R,
Mathews PM, Fraser PE, Westaway D, St
George-Hyslop P, Schmitt-Ulms G (2008)
The in vivo brain interactome of the amyloid
precursor protein. Mol Cell Proteomics
7:15–34
20. Hubner NC, Bird AW, Cox J, Splettstoesser B,
Bandilla P, Poser I, Hyman A, Mann M (2010)
Quantitative proteomics combined with BAC
TransgeneOmics reveals in vivo protein interactions. J Cell Biol 189:739–754
40
Avais M. Daulat et al.
1. Rigaut G, Shevchenko A, Rutz B, Wilm M,
Mann M, Seraphin B (1999) A generic protein
purification method for protein complex characterization and proteome exploration. Nat
Biotechnol 17:1030–1032
2. Daulat AM, Maurice P, Jockers R (2009)
Recent methodological advances in the discovery of GPCR-associated protein complexes.
Trends Pharmacol Sci 30:72–78
3. Ivarsson Y (2012) Plasticity of PDZ domains in
ligand recognition and signaling. FEBS Lett
586:2638–2647
4. te Velthuis AJ, Sakalis PA, Fowler DA,
Bagowski CP (2011) Genome-wide analysis
of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PLoS One 6:e16047
5. Nonaka H, Takei K, Umikawa M, Oshiro M,
Kuninaka K, Bayarjargal M, Asato T,
Yamashiro Y, Uechi Y, Endo S, Suzuki T, Kariya KI (2008) MINK is a Rap2 effector for
phosphorylation of the postsynaptic scaffold
protein TANC1. Biochem Biophys Res Commun 377:573–578
6. Han S, Nam J, Li Y, Kim S, Cho SH, Cho YS,
Choi SY, Choi J, Han K, Kim Y, Na M, Kim H,
Bae YC, Kim E (2010) Regulation of dendritic
spines, spatial memory, and embryonic development by the TANC family of PSD-95-interacting proteins. J Neurosci 30:15102–15112
7. Rabilloud T (1999) Silver staining of 2-D electrophoresis gels. Methods Mol Biol
112:297–305
8. Smaczniak C, Li N, Boeren S, America T, van
Dongen W, Goerdayal SS, de Vries S, Angenent GC, Kaufmann K (2012) Proteomicsbased identification of low-abundance signaling and regulatory protein complexes in native
plant tissues. Nat Protoc 7:2144–2158
9. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass
spectrometry-based shotgun proteomics. Nat
Protoc 11:2301–2319
10. Tyanova S, Temu T, Sinitcyn P, Carlson A,
Hein MY, Geiger T, Mann M, Cox J (2016)
The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat
Methods 13:731–740
11. Tyanova S, Cox J (2018) Perseus: a bioinformatics platform for integrative analysis of proteomics data in cancer research. Methods Mol
Biol 1711:133–148
12. Bouyssie ´ D, Hesse AM, Mouton-Barbosa E,
Rompais M, Macron C, Carapito C, de Peredo
AG, Coute ´ Y, Dupierris V, Burel A, Menetrey
JP, Kalaitzakis A, Poisat J, Romdhani A, BurletSchiltz O, Cianfe ´rani S, Garin J, Bruley C
(2020) Proline: an efficient and user-friendly
software suite for large-scale proteomics. Bioinformatics 36(10):3148–3155
13. Daulat AM, Puvirajesinghe TM, Camoin L,
Borg JP (2018) Mapping cellular polarity networks using mass spectrometry-based strategies. J Mol Biol 430:3545–3564
14. Cartier-Michaud A, Bailly AL, Betzi S, Shi X,
Lissitzky JC, Zarubica A, Serge A, Roche P,
Lugari A, Hamon V, Bardin F, Derviaux C,
Lembo F, Audebert S, Marchetto S,
Durand B, Borg JP, Shi N, Morelli X,
Aurrand-Lions M (2017) Genetic, structural,
and chemical insights into the dual function of
GRASP55 in germ cell Golgi remodeling and
JAM-C polarized localization during spermatogenesis. PLoS Genet 13:e1006803
15. Gagnoux-Palacios L, Awina H, Audebert S,
Rossin A, Mondin M, Borgese F, Planas-BoteyC, Mettouchi A, Borg JP, Hueber AO (2018)
Cell polarity and adherens junction formation
inhibit epithelial Fas cell death receptor signaling. J Cell Biol 217:3839–3852
16. Ernkvist M, Luna Persson N, Audebert S,
Lecine P, Sinha I, Liu M, Schlueter M,
Horowitz A, Aase K, Weide T, Borg JP,
Majumdar A, Holmgren L (2009) The
Amot/Patj/Syx signaling complex spatially
controls RhoA GTPase activity in migrating
endothelial cells. Blood 113:244–253
17. Belotti E, Polanowska J, Daulat AM,
Audebert S, Thome V, Lissitzky JC, Lembo F,
Blibek K, Omi S, Lenfant N, Gangar A,
Montcouquiol M, Santoni MJ, Sebbagh M,
Aurrand-Lions M, Angers S, Kodjabachian L,
Reboul J, Borg JP (2013) The human
PDZome: a gateway to PSD95-Disc
large-zonula occludens (PDZ)-mediated functions. Mol Cell Proteomics 12:2587–2603
18. Mojallal M, Zheng Y, Hultin S, Audebert S,
van Harn T, Johnsson P, Lenander C, Fritz N,
Mieth C, Corcoran M, Lembo F, Hallstrom M,
Hartman J, Mazure NM, Weide T, Grander D,
Borg JP, Uhlen P, Holmgren L (2014)
AmotL2 disrupts apical-basal cell polarity and
promotes tumour invasion. Nat Commun
5:4557
19. Bai Y, Markham K, Chen F, Weerasekera R,
Watts J, Horne P, Wakutani Y, Bagshaw R,
Mathews PM, Fraser PE, Westaway D, St
George-Hyslop P, Schmitt-Ulms G (2008)
The in vivo brain interactome of the amyloid
precursor protein. Mol Cell Proteomics
7:15–34
20. Hubner NC, Bird AW, Cox J, Splettstoesser B,
Bandilla P, Poser I, Hyman A, Mann M (2010)
Quantitative proteomics combined with BAC
TransgeneOmics reveals in vivo protein interactions. J Cell Biol 189:739–754
40
Avais M. Daulat et al.