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Accurate identification of deamidated peptides in global proteomics using a quadrupole orbitrap mass spectrometer.

Nepomuceno AI, Gibson RJ, Randall SM, Muddiman DC.

J Proteome Res. 2014 Feb 7;13(2):777-85. doi: 10.1021/pr400848n.


Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation.

Hao P, Ren Y, Alpert AJ, Sze SK.

Mol Cell Proteomics. 2011 Oct;10(10):O111.009381. doi: 10.1074/mcp.O111.009381.


Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers.

Kalli A, Smith GT, Sweredoski MJ, Hess S.

J Proteome Res. 2013 Jul 5;12(7):3071-86. doi: 10.1021/pr3011588.


Postexperiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS.

Shin B, Jung HJ, Hyung SW, Kim H, Lee D, Lee C, Yu MH, Lee SW.

Mol Cell Proteomics. 2008 Jun;7(6):1124-34. doi: 10.1074/mcp.M700419-MCP200.


Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.

Michalski A, Damoc E, Hauschild JP, Lange O, Wieghaus A, Makarov A, Nagaraj N, Cox J, Mann M, Horning S.

Mol Cell Proteomics. 2011 Sep;10(9):M111.011015. doi: 10.1074/mcp.M111.011015.


Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer.

Kelstrup CD, Young C, Lavallee R, Nielsen ML, Olsen JV.

J Proteome Res. 2012 Jun 1;11(6):3487-97. doi: 10.1021/pr3000249.


Enhanced peptide quantification using spectral count clustering and cluster abundance.

Lee S, Kwon MS, Lee HJ, Paik YK, Tang H, Lee JK, Park T.

BMC Bioinformatics. 2011 Oct 28;12:423. doi: 10.1186/1471-2105-12-423.


Comparative reevaluation of FASP and enhanced FASP methods by LC-MS/MS.

Nel AJ, Garnett S, Blackburn JM, Soares NC.

J Proteome Res. 2015 Mar 6;14(3):1637-42. doi: 10.1021/pr501266c.


Reliable detection of deamidated peptides from lens crystallin proteins using changes in reversed-phase elution times and parent ion masses.

Dasari S, Wilmarth PA, Rustvold DL, Riviere MA, Nagalla SR, David LL.

J Proteome Res. 2007 Sep;6(9):3819-26.


Large precursor tolerance database search - a simple approach for estimation of the amount of spectra with precursor mass shifts in proteomic data.

Weng RR, Chu LJ, Shu HW, Wu TH, Chen MC, Chang Y, Tsai YS, Wilson MC, Tsay YG, Goodlett DR, Ng WV.

J Proteomics. 2013 Oct 8;91:375-84. doi: 10.1016/j.jprot.2013.07.030.


Enhanced separation and characterization of deamidated peptides with RP-ERLIC-based multidimensional chromatography coupled with tandem mass spectrometry.

Hao P, Qian J, Dutta B, Cheow ES, Sim KH, Meng W, Adav SS, Alpert A, Sze SK.

J Proteome Res. 2012 Mar 2;11(3):1804-11. doi: 10.1021/pr201048c.


Quantification of isotopically overlapping deamidated and 18o-labeled peptides using isotopic envelope mixture modeling.

Dasari S, Wilmarth PA, Reddy AP, Robertson LJ, Nagalla SR, David LL.

J Proteome Res. 2009 Mar;8(3):1263-70. doi: 10.1021/pr801054w.


In vivo deamidation characterization of monoclonal antibody by LC/MS/MS.

Huang L, Lu J, Wroblewski VJ, Beals JM, Riggin RM.

Anal Chem. 2005 Mar 1;77(5):1432-9.


A mass spectrometry-based method to screen for α-amidated peptides.

An Z, Chen Y, Koomen JM, Merkler DJ.

Proteomics. 2012 Jan;12(2):173-82. doi: 10.1002/pmic.201100327.


Comparison of the LTQ-Orbitrap Velos and the Q-Exactive for proteomic analysis of 1-1000 ng RAW 264.7 cell lysate digests.

Sun L, Zhu G, Dovichi NJ.

Rapid Commun Mass Spectrom. 2013 Jan 15;27(1):157-62. doi: 10.1002/rcm.6437.


Implementation of Ultraviolet Photodissociation on a Benchtop Q Exactive Mass Spectrometer and Its Application to Phosphoproteomics.

Fort KL, Dyachenko A, Potel CM, Corradini E, Marino F, Barendregt A, Makarov AA, Scheltema RA, Heck AJ.

Anal Chem. 2016 Feb 16;88(4):2303-10. doi: 10.1021/acs.analchem.5b04162.


Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.

Jung HJ, Purvine SO, Kim H, Petyuk VA, Hyung SW, Monroe ME, Mun DG, Kim KC, Park JM, Kim SJ, Tolic N, Slysz GW, Moore RJ, Zhao R, Adkins JN, Anderson GA, Lee H, Camp DG 2nd, Yu MH, Smith RD, Lee SW.

Anal Chem. 2010 Oct 15;82(20):8510-8. doi: 10.1021/ac101388b.


Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer.

Kelstrup CD, Jersie-Christensen RR, Batth TS, Arrey TN, Kuehn A, Kellmann M, Olsen JV.

J Proteome Res. 2014 Dec 5;13(12):6187-95. doi: 10.1021/pr500985w.

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