@article{samaddar_dutta_sinharoy_paul_bhattacharya_saha_chien_goshe_dasgupta_2013, title={Autophosphorylation of gatekeeper tyrosine by symbiosis receptor kinase}, volume={587}, ISSN={["0014-5793"]}, DOI={10.1016/j.febslet.2013.07.050}, abstractNote={Plant receptor‐like kinases (RLKs) share their evolutionary origin with animal interleukin‐1 receptor‐associated kinase (IRAK)/Pelle family of soluble kinases and are distinguished by having tyrosine as ‘gatekeeper’. This position is adjacent to the hinge region and is hidden in a hydrophobic pocket of the catalytic cleft of protein kinases and is therefore least probable to be a target for any modification. This communication illustrates the accessibility of the gatekeeper site (Y670) towards both autophosphorylation and dephosphorylation in the recombinant cytoplasmic domain of symbiosis receptor kinase from Arachis hypogaea (AhSYMRK). Autophosphorylation on gatekeeper tyrosine was detected prior to extraction but never under in vitro conditions. We hypothesize gatekeeper phosphorylation to be associated with synthesis/maturation of AhSYMRK and this phenomenon may be prevalent among RLKs.}, number={18}, journal={FEBS LETTERS}, author={Samaddar, Sandip and Dutta, Ayan and Sinharoy, Senjuti and Paul, Anindita and Bhattacharya, Avisek and Saha, Sudip and Chien, Ko-yi and Goshe, Michael B. and DasGupta, Maitrayee}, year={2013}, month={Sep}, pages={2972–2979} }
 @article{chien_blackburn_liu_goshe_2012, title={Proteomic and Phosphoproteomic Analysis of Chicken Embryo Fibroblasts Infected with Cell Culture-Attenuated and Vaccine Strains of Marek's Disease Virus}, volume={11}, ISSN={["1535-3907"]}, DOI={10.1021/pr300471y}, abstractNote={Vaccination is an effective strategy to reduce the loss of chickens in the poultry industry caused by Marek's Disease (MD), an avian lymphoproliferative disease. The vaccines currently used are from attenuated serotype 1 Marek's disease virus (MDV) or naturally nononcogenic MDV strains. To prepare for future immunity breaks, functional genomic and proteomic studies have been used to better understand the underlying mechanisms of MDV pathogenicity and the effects induced by the vaccine viruses. In this study, a combined approach of quantitative GeLC-MSE and qualitative ERLIC/IMAC/LC-MS/MS analysis were used to identify abundance changes of proteins and the variations of phosphorylation status resulting from the perturbations due to infection with an attenuated oncogenic virus strain (Md11/75C) and several nononcogenic virus strains (CVI988, FC126 and 301B) in vitro. Using this combined approach, several signal transduction pathways mapped by the identified proteins were found to be altered at both the level of protein abundance and phosphorylation. On the basis of this study, a kinase-dependent pathway to regulate phosphorylation of 4E-BP1 to modulate assembly of the protein translation initiation complex was revealed. The differences of 4E-BP1 phosphorylation patterns as well as the measured abundance changes among several other proteins that regulate host transcriptional and translational activities across the virus strains used in this study provide new insight for future functional and biochemical characterization of specific proteins involved in MDV pathogenesis.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Chien, Ko-yi and Blackburn, Kevin and Liu, Hsiao-Ching and Goshe, Michael B.}, year={2012}, month={Dec}, pages={5663–5677} }
 @article{chien_liu_goshe_2011, title={Development and Application of a Phosphoproteomic Method Using Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC), IMAC, and LC-MS/MS Analysis to Study Marek's Disease Virus Infection}, volume={10}, ISSN={["1535-3893"]}, DOI={10.1021/pr2002403}, abstractNote={Marek's Disease (MD) is an avian neoplastic disease caused by Marek's Disease Virus (MDV). The mechanism of virus transition between the lytic and latent cycle is still being investigated; however, post-translational modifications, especially phosphorylation, have been thought to play an important role. Previously, our group has used strong cation exchange chromatography in conjunction with reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the changes in global proteomic expression upon MDV infection (Ramaroson , M. F.; Ruby, J.; Goshe, M. B.; Liu , H.-C. S. J. Proteome Res. 2008, 7, 4346-4358). Here, we extend our study by developing an effective separation and enrichment approach to investigate the changes occurring in the phosphoproteome using electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) to fractionate peptides from chicken embryo fibroblast (CEF) digests and incorporating a subsequent IMAC enrichment step to selectively target phosphorylated peptides for LC-MS/MS analysis. To monitor the multidimensional separation between mock- and MDV-infected CEF samples, a casein phosphopeptide mixture was used as an internal standard. With LC-MS/MS analysis alone, no CEF phosphopeptides were detected, while with ERLIC fractionation only 1.2% of all identified peptides were phosphorylated. However, the incorporation of IMAC enrichment with ERLIC fractionation provided a 50-fold increase in the percentage of identified phosphopeptides. Overall, a total of 581 unique phosphopeptides were identified (p < 0.05) with those of the MDV-infected CEF sample containing nearly twice as many as the mock-infected control of which 11% were unique to MDV proteins. The changes in the phosphoproteome are discussed including the role that microtubule-associated proteins may play in MDV infection mechanisms.}, number={9}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Chien, Ko-yi and Liu, Hsiao-Ching and Goshe, Michael B.}, year={2011}, month={Sep}, pages={4041–4053} }
 @misc{chien_goshe_2009, title={Advances in Quantitative Mass Spectrometry Analysis: Weighing in on Isotope Coding and Label-Free Approaches for Expression and Functional Proteomics}, volume={5}, ISSN={["1875-6727"]}, DOI={10.2174/157341109787846126}, abstractNote={Mass spectrometry is an extremely versatile analytical technique that is capable of characterizing proteins at various levels of biochemical sophistication from recognition of protein components and their modifications to their quantification within a sample. With the development of electrospray ionization and matrix-assisted laser desorption ionization, the last decade of protein analysis using mass spectrometry has fully established the field of proteomics within the life sciences and a major player in the systems biology paradigm. The diversity of proteins and their multi-facetted functions are indicative of the numerous mass spectrometry methods that are used in quantitative proteomic analysis. In this review, the various techniques developed to quantify protein abundance by mass spectrometry are presented in terms of those associated with both stable isotope coding and label-free strategies. The implementation of these methods to the quantitative mass spectrometry analysis from “proof-of-concept” to those that tackle investigations of protein expression and those of protein function mediated by post-translation modifications are also discussed. Keywords: Mass spectrometry, Quantitative proteomics, Phosphoproteomics, Isotope coding, Label-free quantitation, Absolute quantitation}, number={2}, journal={CURRENT ANALYTICAL CHEMISTRY}, author={Chien, Ko-yi and Goshe, Michael B.}, year={2009}, month={Apr}, pages={166–185} }