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Introduction

MsViz, a zero learning curve graphical software tool for detailed manual validation and quantitation of post-translational modifications - RM - 2016
Filtering and scoring of results from AP-MS experiments by spectral counts,label-freequantitation and enrichment factor - RM - 2015
Onco-proteomics approach to identify novel protein variants in databases derived from individual melanoma sequenced genomes - PW - 2012
Slice SILAC : coupling isotope labeling with electrophoretic migration to study protein processing events - MQ
A Common Processing and Statistical Framework for Label-Free Quantitative Proteomic Analyses - PW - 2009
Background proteins in immunoprecipitations: what they are & how to reduce them - MQ - 2009

SLICE SILAC source code: Morikawa K, et al. Hepatology 2014, 59(2): 423-433, PMID:23929719.
Data processing scripts : Borgatta M, et al. J Proteome Res. 2015, 14(1), 279-291, PMID: 25350372.