205
High-Resolution Proteomic Analyses
2019 Jun 3;2019(6). doi: 10.1101/pdb.prot098376. PMID:
30104410.
Lombard-Banek C, Reddy S, Moody SA, Nemes P. Label-free
quantifcation of proteins in single embryonic cells with neural fate in the cleavage-stage frog ( Xenopus laevis ) embryo
using capillary electrophoresis electrospray ionization highresolution mass spectrometry (CE-ESI-HRMS). Mol Cell
Proteomics. 2016 Aug;15(8):2756–2768. doi: 10.1074/mcp.
M115.057760. PMID: 27317400; PMCID: PMC4974349.
Martin MT. Methods and Compositions for Reverse Translation.
2006. patents.google.com/patent/US7169894
McGivern JV, Swaney DL, Coon JJ, Sheets MD. Toward def ning the phosphoproteome of Xenopus laevis embryos. Dev
Dyn. 2009 Jun;238(6):1433–1443. doi: 10.1002/dvdy.21941.
PMID: 19384857; PMCID: PMC2865133.
Naert T, Tulkens D, Edwards NA, Carron M, Shaidani NI, Wizla
M, Boel A, Demuynck S, Horb ME, Coucke P, Willaert A,
Zorn AM, Vleminckx K. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafsh embryos. Sci Rep. 2020 Sep
4;10(1):14662. doi: 10.1038/s41598-020-71412-0. PMID:
32887910; PMCID: PMC7473854.
Nakayama T, Blitz IL, Fish MB, Odeleye AO, Manohar S, Cho KW,
Grainger RM. Cas9-based genome editing in Xenopus tropicalis. Methods Enzymol. 2014;546:355–375. doi: 10.1016/
B978-0-12-801185-0.00017-9. PMID: 25398349; PMCID:
PMC4284096.
Nashimoto M. The RNA/protein symmetry hypothesis:
Experimental support for reverse translation of primitive
proteins. J Theor Biol. 2001 Mar 21;209(2):181–187. doi:
10.1006/jtbi.2000.2253. PMID: 11401460.
Nieuwkoop PD, Faber J. Normal Table of Xenopus laevis
(Daudin). 1994. Garland Publishing Inc, New York ISBN
0-8153-1896-0.
Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML,
Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S,
Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.
Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.
2000475. PMID: 20068231.
Onjiko RM, Moody SA, Nemes P. Single-cell mass spectrometry
reveals small molecules that affect cell fates in the 16-cell
embryo. Proc Natl Acad Sci USA. 2015 May 26;112(21):6545–
6550. doi: 10.1073/pnas.1423682112. PMID: 25941375; PMC
ID: PMC4450407.
Pennisi E. Development cell by cell. Science. 2018 Dec 21;
362(6421):1344–1345. doi: 10.1126/science.362.6421.1344.
PMID: 30573610.
Peshkin L, Gupta M, Ryazanova L, Wühr M. Bayesian confdence intervals for multiplexed proteomics integrate
ion-statistics with peptide quantif cation concordance.
Mol Cell Proteomics. 2019a Oct;18(10):2108–2120. doi:
10.1074/mcp.TIR119.001317. PMID: 31311848; PMCID:
PMC6773559.
Peshkin L, Lukyanov A, Kalocsay M, Gage RM, Wang DZ, Pells
TJ, Karimi K, Vize PD, Wühr M, Kirschner MW. The protein repertoire in early vertebrate embryogenesis. BioRxiv.
2019b:571174. doi.org/10.1101/571174.
Peshkin L, Wühr M, Pearl E, Haas W, Freeman RM Jr, Gerhart
JC, Klein AM, Horb M, Gygi SP, Kirschner MW. On the
relationship of protein and mRNA dynamics in vertebrate
embryonic development. Dev Cell. 2015 Nov 9;35(3):383–
394. doi: 10.1016/j.devcel.2015.10.010. PMID: 26555057;
PMCID: PMC4776761.
Peuchen EH, Cox OF, Sun L, Hebert AS, Coon JJ, Champion MM,
Dovichi NJ, Huber PW. Phosphorylation dynamics dominate
the regulated proteome during early Xenopus development.
Sci Rep. 2017 Nov 15;7(1):15647. doi: 10.1038/s41598-01715936-y. PMID: 29142207; PMCID: PMC5688136.
Peuchen EH, Sun L, Dovichi NJ. Optimization and comparison of bottom-up proteomic sample preparation for earlystage Xenopus laevis embryos. Anal Bioanal Chem. 2016
Jul;408(17):4743–4749. doi: 10.1007/s00216-016-9564-2.
PMID: 27137514; PMCID: PMC4926613.
Presler M, Van Itallie E, Klein AM, Kunz R, Coughlin ML,
Peshkin L, Gygi SP, Wühr M, Kirschner MW. Proteomics
of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. Proc Natl Acad Sci
USA. 2017 Dec 12;114(50):E10838–E10847. doi: 10.1073/
pnas.1709207114. PMID: 29183978; PMCID: PMC5740657.
Qu Y, Dubiak KM, Peuchen EH, Champion MM, Zhang Z, Hebert
AS, Wright S, Coon JJ, Huber PW, Dovichi NJ. Quantitative
capillary zone electrophoresis-mass spectrometry reveals
the N-glycome developmental plan during vertebrate
embryogenesis. Mol Omics. 2020 Jun 15;16(3):210–220.
doi: 10.1039/d0mo00005a. PMID: 32149324; PMCID:
PMC7299754.
Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen
PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev
B. System-wide temporal characterization of the proteome
and phosphoproteome of human embryonic stem cell differentiation. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/
scisignal.2001570. PMID: 21406692.
Saha-Shah A, Esmaeili M, Sidoli S, Hwang H, Yang J, Klein PS,
Garcia BA. Single cell proteomics by data-independent
acquisition to study embryonic asymmetry in Xenopus
laevis. Anal Chem. 2019 Jul 16;91(14):8891–8899. doi:
10.1021/acs.analchem.9b00327. PMID: 31194517; PMCID:
PMC6688503.
Savova V, Pearl EJ, Boke E, Nag A, Adzhubei I, Horb ME, Peshkin
L. Transcriptomic insights into genetic diversity of proteincoding genes in X. laevis. Dev Biol. 2017 Apr 15;424(2):181–
188. doi: 10.1016/j.ydbio.2017.02.019. PMID: 28283406;
PMCID: PMC5405699.
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi
S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen
SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons
JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T,
Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou
G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J,
Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood
J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto
Y, Yamamoto TS, Takagi C, Heald R, Miller K, Houston
DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M,
Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N,
Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M,
Rokhsar DS. Genome evolution in the allotetraploid frog
Xenopus laevis. Nature. 2016 Oct 20;538(7625):336–343.
doi: 10.1038/nature19840. PMID: 27762356; PMCID:
PMC5313049.
Sheets MD, Fritz B, Hartley RS, Zhang Y. Polyribosome analysis for investigating mRNA translation in Xenopus oocytes,
eggs and embryos. Methods. 2010 May;51(1):152–156. doi:
10.1016/j.ymeth.2010.01.023. PMID: 20096782; PMCID:
PMC2868116.
Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra
GJ, Vermeulen M. Global absolute quantif cation reveals
tight regulation of protein expression in single Xenopus eggs.
High-Resolution Proteomic Analyses
2019 Jun 3;2019(6). doi: 10.1101/pdb.prot098376. PMID:
30104410.
Lombard-Banek C, Reddy S, Moody SA, Nemes P. Label-free
quantifcation of proteins in single embryonic cells with neural fate in the cleavage-stage frog ( Xenopus laevis ) embryo
using capillary electrophoresis electrospray ionization highresolution mass spectrometry (CE-ESI-HRMS). Mol Cell
Proteomics. 2016 Aug;15(8):2756–2768. doi: 10.1074/mcp.
M115.057760. PMID: 27317400; PMCID: PMC4974349.
Martin MT. Methods and Compositions for Reverse Translation.
2006. patents.google.com/patent/US7169894
McGivern JV, Swaney DL, Coon JJ, Sheets MD. Toward def ning the phosphoproteome of Xenopus laevis embryos. Dev
Dyn. 2009 Jun;238(6):1433–1443. doi: 10.1002/dvdy.21941.
PMID: 19384857; PMCID: PMC2865133.
Naert T, Tulkens D, Edwards NA, Carron M, Shaidani NI, Wizla
M, Boel A, Demuynck S, Horb ME, Coucke P, Willaert A,
Zorn AM, Vleminckx K. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafsh embryos. Sci Rep. 2020 Sep
4;10(1):14662. doi: 10.1038/s41598-020-71412-0. PMID:
32887910; PMCID: PMC7473854.
Nakayama T, Blitz IL, Fish MB, Odeleye AO, Manohar S, Cho KW,
Grainger RM. Cas9-based genome editing in Xenopus tropicalis. Methods Enzymol. 2014;546:355–375. doi: 10.1016/
B978-0-12-801185-0.00017-9. PMID: 25398349; PMCID:
PMC4284096.
Nashimoto M. The RNA/protein symmetry hypothesis:
Experimental support for reverse translation of primitive
proteins. J Theor Biol. 2001 Mar 21;209(2):181–187. doi:
10.1006/jtbi.2000.2253. PMID: 11401460.
Nieuwkoop PD, Faber J. Normal Table of Xenopus laevis
(Daudin). 1994. Garland Publishing Inc, New York ISBN
0-8153-1896-0.
Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML,
Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S,
Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.
Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.
2000475. PMID: 20068231.
Onjiko RM, Moody SA, Nemes P. Single-cell mass spectrometry
reveals small molecules that affect cell fates in the 16-cell
embryo. Proc Natl Acad Sci USA. 2015 May 26;112(21):6545–
6550. doi: 10.1073/pnas.1423682112. PMID: 25941375; PMC
ID: PMC4450407.
Pennisi E. Development cell by cell. Science. 2018 Dec 21;
362(6421):1344–1345. doi: 10.1126/science.362.6421.1344.
PMID: 30573610.
Peshkin L, Gupta M, Ryazanova L, Wühr M. Bayesian confdence intervals for multiplexed proteomics integrate
ion-statistics with peptide quantif cation concordance.
Mol Cell Proteomics. 2019a Oct;18(10):2108–2120. doi:
10.1074/mcp.TIR119.001317. PMID: 31311848; PMCID:
PMC6773559.
Peshkin L, Lukyanov A, Kalocsay M, Gage RM, Wang DZ, Pells
TJ, Karimi K, Vize PD, Wühr M, Kirschner MW. The protein repertoire in early vertebrate embryogenesis. BioRxiv.
2019b:571174. doi.org/10.1101/571174.
Peshkin L, Wühr M, Pearl E, Haas W, Freeman RM Jr, Gerhart
JC, Klein AM, Horb M, Gygi SP, Kirschner MW. On the
relationship of protein and mRNA dynamics in vertebrate
embryonic development. Dev Cell. 2015 Nov 9;35(3):383–
394. doi: 10.1016/j.devcel.2015.10.010. PMID: 26555057;
PMCID: PMC4776761.
Peuchen EH, Cox OF, Sun L, Hebert AS, Coon JJ, Champion MM,
Dovichi NJ, Huber PW. Phosphorylation dynamics dominate
the regulated proteome during early Xenopus development.
Sci Rep. 2017 Nov 15;7(1):15647. doi: 10.1038/s41598-01715936-y. PMID: 29142207; PMCID: PMC5688136.
Peuchen EH, Sun L, Dovichi NJ. Optimization and comparison of bottom-up proteomic sample preparation for earlystage Xenopus laevis embryos. Anal Bioanal Chem. 2016
Jul;408(17):4743–4749. doi: 10.1007/s00216-016-9564-2.
PMID: 27137514; PMCID: PMC4926613.
Presler M, Van Itallie E, Klein AM, Kunz R, Coughlin ML,
Peshkin L, Gygi SP, Wühr M, Kirschner MW. Proteomics
of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. Proc Natl Acad Sci
USA. 2017 Dec 12;114(50):E10838–E10847. doi: 10.1073/
pnas.1709207114. PMID: 29183978; PMCID: PMC5740657.
Qu Y, Dubiak KM, Peuchen EH, Champion MM, Zhang Z, Hebert
AS, Wright S, Coon JJ, Huber PW, Dovichi NJ. Quantitative
capillary zone electrophoresis-mass spectrometry reveals
the N-glycome developmental plan during vertebrate
embryogenesis. Mol Omics. 2020 Jun 15;16(3):210–220.
doi: 10.1039/d0mo00005a. PMID: 32149324; PMCID:
PMC7299754.
Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen
PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev
B. System-wide temporal characterization of the proteome
and phosphoproteome of human embryonic stem cell differentiation. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/
scisignal.2001570. PMID: 21406692.
Saha-Shah A, Esmaeili M, Sidoli S, Hwang H, Yang J, Klein PS,
Garcia BA. Single cell proteomics by data-independent
acquisition to study embryonic asymmetry in Xenopus
laevis. Anal Chem. 2019 Jul 16;91(14):8891–8899. doi:
10.1021/acs.analchem.9b00327. PMID: 31194517; PMCID:
PMC6688503.
Savova V, Pearl EJ, Boke E, Nag A, Adzhubei I, Horb ME, Peshkin
L. Transcriptomic insights into genetic diversity of proteincoding genes in X. laevis. Dev Biol. 2017 Apr 15;424(2):181–
188. doi: 10.1016/j.ydbio.2017.02.019. PMID: 28283406;
PMCID: PMC5405699.
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi
S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen
SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons
JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T,
Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou
G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J,
Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood
J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto
Y, Yamamoto TS, Takagi C, Heald R, Miller K, Houston
DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M,
Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N,
Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M,
Rokhsar DS. Genome evolution in the allotetraploid frog
Xenopus laevis. Nature. 2016 Oct 20;538(7625):336–343.
doi: 10.1038/nature19840. PMID: 27762356; PMCID:
PMC5313049.
Sheets MD, Fritz B, Hartley RS, Zhang Y. Polyribosome analysis for investigating mRNA translation in Xenopus oocytes,
eggs and embryos. Methods. 2010 May;51(1):152–156. doi:
10.1016/j.ymeth.2010.01.023. PMID: 20096782; PMCID:
PMC2868116.
Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra
GJ, Vermeulen M. Global absolute quantif cation reveals
tight regulation of protein expression in single Xenopus eggs.