Data Collection with Automated Precursor Ion Exclusion:

Zhang, Z. Automated Precursor Ion Exclusion During LC/MS/MS Data Acquisition for Optimal Ion Identification. J. Am. Soc. Mass Spectrom. 2012, 23(8), 1400−1407.

Large-Scale Identification/Quantification of Modifications:

Zhang, Z. Large-scale Identification and Quantification of Covalent Modifications in Therapeutic Proteins. Anal. Chem. 2009, 81(20), 8354−8364.

Peptide Identification by CID MS/MS Prediction:

Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 2004, 76(14), 3908−3922.

Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 2005, 77(19), 6364−6373.

Zhang, Z. and Shah, B. Prediction of collision-induced dissociation spectra of common N-glycopeptides for glycoform identification. Anal. Chem. 2010, 82(24), 10194−10202.

Zhang, Z. Prediction of collision-induced dissociation spectra of peptides with post-translational or process-induced modifications. Anal. Chem. 2011, 83(22), 8642−8651.

Peptide Identification by ETD/ECD MS/MS Prediction:

Zhang, Z. Prediction of electron-transfer/capture dissociation spectra of peptides. Anal. Chem. 2010, 82(5), 1990−2005.

Retention Time Alignment:

Zhang, Z. Retention time alignment of LC/MS data by a divide-and-conquer algorithm. J. Am. Soc. Mass Spectrom. 2012, 23(4), 764−772.

Protein Theoretical Mass Calculation:

Zhang, Z., Pan, H. and Chen, X. Mass spectrometry for structural characterization of therapeutic antibodies. Mass Spectrom. Reviews. 2009, 28(1), 147−176.

Spectral Processing:

Zhang, Z. and McElvain, J. S. Optimizing spectroscopic signal-to-noise ratio in analysis of data collected by a chromatographic/spectroscopic system. Anal. Chem. 1999, 71(1), 39−45.

Charge and Mass Determination:

Zhang, Z. and Marshall, A. G. A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra. J. Am. Soc. Mass Spectrom. 1998, 9(3), 225−233.

Top-Down Protein Characterization:

Zhang, Z. and Shah, B. Characterization of variable regions of monoclonal antibodies by top-down mass spectrometry. Anal. Chem. 2007, 79(15), 5723−5729.

H/D Exchange Data Processing:

Zhang, Z., Zhang, A. and Xiao, G. Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing. Anal. Chem. 2012, 84(11), 4942−4949.

Oligonucleotide and mRNA Analysis:

Vanhinsbergh, C. J., Criscuolo, A., Sutton, J. N., Murphy, K., Williamson, A. J. K., Cook, K. and Dickman, M. J. Characterization and sequence mapping of large RNA and mRNA therapeutics using mass spectrometry. Anal. Chem. 2022, 94(20), 7339–7349.