22. Mimae T, Ito A (2015) New challenges in
pseudopodial proteomics by a laser-assisted
cell etching technique. Biochim Biophys Acta
1854:538–546
23. Gousset K, Marzo L, Commere P, Zurzolo C
(2013) Myo10 is a key regulator of TNT formation in neuronal cells. J Cell Sci
126:4424–4435
24. Eltoum I, Fredenburgh J, Myers RB, Grizzle
WE (2001) Introduction to the theory and
practice of fixation of tissues. J Histotechnol
24:173–190
25. Gosselin MA, Guo W, Lee RJ (2001) Efficient
gene transfer using reversibly cross-linked low
molecular weight polyethylenimine. Bioconjug
Chem 12:989–994
26. Gordon A, Kannan SK, Gousset K (2018) A
novel cell fixation method that greatly
enhances protein identification in microproteomic studies using laser capture microdissection and mass spectrometry. Proteomics 18:
e1700294
27. Gousset K, Gordon A, Kumar Kannan S, Tovar
J (2019) A novel microproteomic approach
using laser capture microdissection to study
cellular protrusions. Int J Mol Sci 20:1172
28. Osswald M, Jung E, Sahm F et al (2015) Brain
tumour cells interconnect to a functional and
resistant network. Nature 528:93–98
29. Desir S, Dickson EL, Vogel RI et al (2016)
Tunneling nanotube formation is stimulated
by hypoxia in ovarian cancer cells. Oncotarget.
https://doi.org/10.18632/oncotarget.9504
30. Hashimoto M, Bhuyan F, Hiyoshi M et al
(2016) Potential role of the formation of tunneling nanotubes in HIV-1 spread in macrophages. J Immunol 196:1832–1841
31. Victoria GS, Arkhipenko A, Zhu S et al (2016)
Astrocyte-to-neuron intercellular prion transfer is mediated by cell-cell contact. Sci Rep
6:20762
32. Levin Y (2011) The role of statistical power
analysis in quantitative proteomics. Proteomics
11:2565–2567.
https://doi.org/10.1002/
pmic.201100033
33. Arike L, Peil L (2014) Spectral counting labelfree proteomics. Methods Mol Biol
1156:213–222
34. McIlwain S, Mathews M, Bereman MS, Rubel
EW, MacCoss MJ, Noble WS (2012) Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinformatics
13:308.
https://doi.org/10.1186/14712105-13-308
35. Wang M, Zhao Y, Zhang B (2015) Efficient
test and visualization of multiset intersections.
Sci Rep 5:16923
36. Huang DW, Sherman BT, Lempicki RA (2009)
Systematic and integrative analysis of large gene
lists using DAVID Bioinformatics Resources.
Nat Protoc 4:44–57
37. Huang DW, Sherman BT, Lempicki RA (2009)
Bioinformatics enrichment tools: paths toward
the comprehensive functional analysis of large
gene lists. Nucleic Acids Res 37:1–13
38. Liebermeister W, Noor E, Flamholz A,
Davidi D, Bernhardt J, Milo R (2014) Visual
account of protein investment in cellular functions. Proc Natl Acad Sci U S A
111:8488–8493
39. Mi H, Muruganujan A, Ebert D, Huang X,
Thomas PD (2019) PANTHER version 14:
more genomes, a new PANTHER GO-slim
and improvements in enrichment analysis
tools. Nucleic Acids Res 47:D419–D426.
https://doi.org/10.1093/nar/gky1038
40. Eden E, Navon R, Steinfeld I, Lipson D,
Yakhini Z (2009) GOrilla: a tool for discovery
and visualization of enriched GO terms in
ranked gene lists. BMC Bioinformatics 10:48
41. Eden E, Lipson D, Yogev S, Yakhini Z (2007)
Discovering motifs in ranked lists of DNA
sequences. PLoS Comput Biol 3:e39
Proteome of Cellular Protrusions Identified by LCM/MS
45
pseudopodial proteomics by a laser-assisted
cell etching technique. Biochim Biophys Acta
1854:538–546
23. Gousset K, Marzo L, Commere P, Zurzolo C
(2013) Myo10 is a key regulator of TNT formation in neuronal cells. J Cell Sci
126:4424–4435
24. Eltoum I, Fredenburgh J, Myers RB, Grizzle
WE (2001) Introduction to the theory and
practice of fixation of tissues. J Histotechnol
24:173–190
25. Gosselin MA, Guo W, Lee RJ (2001) Efficient
gene transfer using reversibly cross-linked low
molecular weight polyethylenimine. Bioconjug
Chem 12:989–994
26. Gordon A, Kannan SK, Gousset K (2018) A
novel cell fixation method that greatly
enhances protein identification in microproteomic studies using laser capture microdissection and mass spectrometry. Proteomics 18:
e1700294
27. Gousset K, Gordon A, Kumar Kannan S, Tovar
J (2019) A novel microproteomic approach
using laser capture microdissection to study
cellular protrusions. Int J Mol Sci 20:1172
28. Osswald M, Jung E, Sahm F et al (2015) Brain
tumour cells interconnect to a functional and
resistant network. Nature 528:93–98
29. Desir S, Dickson EL, Vogel RI et al (2016)
Tunneling nanotube formation is stimulated
by hypoxia in ovarian cancer cells. Oncotarget.
https://doi.org/10.18632/oncotarget.9504
30. Hashimoto M, Bhuyan F, Hiyoshi M et al
(2016) Potential role of the formation of tunneling nanotubes in HIV-1 spread in macrophages. J Immunol 196:1832–1841
31. Victoria GS, Arkhipenko A, Zhu S et al (2016)
Astrocyte-to-neuron intercellular prion transfer is mediated by cell-cell contact. Sci Rep
6:20762
32. Levin Y (2011) The role of statistical power
analysis in quantitative proteomics. Proteomics
11:2565–2567.
https://doi.org/10.1002/
pmic.201100033
33. Arike L, Peil L (2014) Spectral counting labelfree proteomics. Methods Mol Biol
1156:213–222
34. McIlwain S, Mathews M, Bereman MS, Rubel
EW, MacCoss MJ, Noble WS (2012) Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinformatics
13:308.
https://doi.org/10.1186/14712105-13-308
35. Wang M, Zhao Y, Zhang B (2015) Efficient
test and visualization of multiset intersections.
Sci Rep 5:16923
36. Huang DW, Sherman BT, Lempicki RA (2009)
Systematic and integrative analysis of large gene
lists using DAVID Bioinformatics Resources.
Nat Protoc 4:44–57
37. Huang DW, Sherman BT, Lempicki RA (2009)
Bioinformatics enrichment tools: paths toward
the comprehensive functional analysis of large
gene lists. Nucleic Acids Res 37:1–13
38. Liebermeister W, Noor E, Flamholz A,
Davidi D, Bernhardt J, Milo R (2014) Visual
account of protein investment in cellular functions. Proc Natl Acad Sci U S A
111:8488–8493
39. Mi H, Muruganujan A, Ebert D, Huang X,
Thomas PD (2019) PANTHER version 14:
more genomes, a new PANTHER GO-slim
and improvements in enrichment analysis
tools. Nucleic Acids Res 47:D419–D426.
https://doi.org/10.1093/nar/gky1038
40. Eden E, Navon R, Steinfeld I, Lipson D,
Yakhini Z (2009) GOrilla: a tool for discovery
and visualization of enriched GO terms in
ranked gene lists. BMC Bioinformatics 10:48
41. Eden E, Lipson D, Yogev S, Yakhini Z (2007)
Discovering motifs in ranked lists of DNA
sequences. PLoS Comput Biol 3:e39
Proteome of Cellular Protrusions Identified by LCM/MS
45