and multiply phosphorylated peptides from a
single titanium dioxide microcolumn. Anal
Chem 87:10213–10221
10. Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR,
Shah P, Gillette MA, Petyuk VA, Thomas SN,
Mani DR, Mundt F, Moore RJ, Hu Y, Zhao R,
Schnaubelt M, Keshishian H, Monroe ME,
Zhang Z, Udeshi ND, Mani D, Davies SR,
Townsend RR, Chan DW, Smith RD,
Zhang H, Liu T, Carr SA (2018) Reproducible
workflow for multiplexed deep-scale proteome
and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nat Protoc 13:1632–1661
11. Hogrebe A, von Stechow L, Bekker-Jensen
DB, Weinert BT, Kelstrup CD, Olsen JV
(2018) Benchmarking common quantification
strategies for large-scale phosphoproteomics.
Nat Commun 9:1045
12. Yi L, Tsai CF, Dirice E, Swensen AC, Chen J,
Shi T, Gritsenko MA, Chu RK, Piehowski PD,
Smith RD, Rodland KD, Atkinson MA, Mathews CE, Kulkarni RN, Liu T, Qian WJ (2019)
A boosting to amplify signal with isobaric labeling (BASIL) strategy for comprehensive quantitative phosphoproteomic characterization of
small populations of cells. Anal Chem
91:5794–5801
13. Giansanti P, Aye TT, van den Toorn H,
Peng M, van Breukelen B, Heck AJ (2015)
An
augmented
multiple-protease-based
human phosphopeptide atlas. Cell Rep
11:1834–1843
14. Olsen JV, Ong SE, Mann M (2004) Trypsin
cleaves exclusively C-terminal to arginine and
lysine residues. Mol Cell Proteomics
3:608–614
15. Tsai CF, Smith JS, Krajewski K, Zhao R,
Moghieb AM, Nicora CD, Xiong X, Moore
RJ, Liu T, Smith RD, Jacobs JM, Rajagopal S,
Shi T (2019) Tandem mass tag labeling facilitates reversed-phase liquid chromatographymass spectrometry analysis of hydrophilic
phosphopeptides.
Anal
Chem
91:11606–11613
16. Cox J, Mann M (2008) MaxQuant enables
high peptide identification rates, individualized
p.p.b.-range mass accuracies and proteomewide protein quantification. Nat Biotechnol
26:1367–1372
17. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass
spectrometry-based shotgun proteomics. Nat
Protoc 11:2301–2319
18. Zecha J, Satpathy S, Kanashova T, Avanessian
SC, Kane MH, Clauser KR, Mertins P, Carr SA,
Kuster B (2019) TMT labeling for the masses:
a robust and cost-efficient, in-solution labeling
approach. Mol Cell Proteomics 18:1468–1478
Analysis of Hydrophilic Phosphopeptides
257
single titanium dioxide microcolumn. Anal
Chem 87:10213–10221
10. Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR,
Shah P, Gillette MA, Petyuk VA, Thomas SN,
Mani DR, Mundt F, Moore RJ, Hu Y, Zhao R,
Schnaubelt M, Keshishian H, Monroe ME,
Zhang Z, Udeshi ND, Mani D, Davies SR,
Townsend RR, Chan DW, Smith RD,
Zhang H, Liu T, Carr SA (2018) Reproducible
workflow for multiplexed deep-scale proteome
and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nat Protoc 13:1632–1661
11. Hogrebe A, von Stechow L, Bekker-Jensen
DB, Weinert BT, Kelstrup CD, Olsen JV
(2018) Benchmarking common quantification
strategies for large-scale phosphoproteomics.
Nat Commun 9:1045
12. Yi L, Tsai CF, Dirice E, Swensen AC, Chen J,
Shi T, Gritsenko MA, Chu RK, Piehowski PD,
Smith RD, Rodland KD, Atkinson MA, Mathews CE, Kulkarni RN, Liu T, Qian WJ (2019)
A boosting to amplify signal with isobaric labeling (BASIL) strategy for comprehensive quantitative phosphoproteomic characterization of
small populations of cells. Anal Chem
91:5794–5801
13. Giansanti P, Aye TT, van den Toorn H,
Peng M, van Breukelen B, Heck AJ (2015)
An
augmented
multiple-protease-based
human phosphopeptide atlas. Cell Rep
11:1834–1843
14. Olsen JV, Ong SE, Mann M (2004) Trypsin
cleaves exclusively C-terminal to arginine and
lysine residues. Mol Cell Proteomics
3:608–614
15. Tsai CF, Smith JS, Krajewski K, Zhao R,
Moghieb AM, Nicora CD, Xiong X, Moore
RJ, Liu T, Smith RD, Jacobs JM, Rajagopal S,
Shi T (2019) Tandem mass tag labeling facilitates reversed-phase liquid chromatographymass spectrometry analysis of hydrophilic
phosphopeptides.
Anal
Chem
91:11606–11613
16. Cox J, Mann M (2008) MaxQuant enables
high peptide identification rates, individualized
p.p.b.-range mass accuracies and proteomewide protein quantification. Nat Biotechnol
26:1367–1372
17. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass
spectrometry-based shotgun proteomics. Nat
Protoc 11:2301–2319
18. Zecha J, Satpathy S, Kanashova T, Avanessian
SC, Kane MH, Clauser KR, Mertins P, Carr SA,
Kuster B (2019) TMT labeling for the masses:
a robust and cost-efficient, in-solution labeling
approach. Mol Cell Proteomics 18:1468–1478
Analysis of Hydrophilic Phosphopeptides
257