@article{mitra_chen_dhandaydham_wang_blackburn_kota_goshe_schwartz_huber_clouse_2015, title={An autophosphorylation site database for leucine-rich repeat receptor-like kinases in Arabidopsis thaliana}, volume={82}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.12863}, abstractNote={Summary}, number={6}, journal={PLANT JOURNAL}, author={Mitra, Srijeet K. and Chen, Ruiqiang and Dhandaydham, Murali and Wang, Xiaofeng and Blackburn, Robert Kevin and Kota, Uma and Goshe, Michael B. and Schwartz, Daniel and Huber, Steven C. and Clouse, Steven D.}, year={2015}, month={Jun}, pages={1042–1060} }
 @article{bajwa_wang_blackburn_goshe_mitra_williams_bishop_krasnyanski_allen_huber_et al._2013, title={Identification and Functional Analysis of Tomato BRI1 and BAK1 Receptor Kinase Phosphorylation Sites}, volume={163}, ISSN={["1532-2548"]}, DOI={10.1104/pp.113.221465}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Bajwa, Vikramjit S. and Wang, Xiaofeng and Blackburn, R. Kevin and Goshe, Michael B. and Mitra, Srijeet K. and Williams, Elisabeth L. and Bishop, Gerard J. and Krasnyanski, Sergei and Allen, George and Huber, Steven C. and et al.}, year={2013}, month={Sep}, pages={30–42} }
 @article{blackburn_mbeunkui_mitra_mentzel_goshe_2010, title={Improving Protein and Proteome Coverage through Data-Independent Multiplexed Peptide Fragmentation}, volume={9}, ISSN={["1535-3907"]}, DOI={10.1021/pr100144z}, abstractNote={Performance differences in protein and proteome characterization achieved by data-independent acquisition (DIA) LC/MS(E) and data-dependent acquisition (DDA) LC/MS/MS approaches were investigated. LC/MS(E) is a novel mode of generating product ion data for all coeluting precursors in parallel as opposed to LC/MS/MS where coeluting precursors must be serially fragmented one at a time. During LC/MS(E) analysis, alternating MS scans of "normal" and "elevated" collision energy are collected at regular intervals, providing nearly a 100% duty cycle for precursor detection and fragmentation because all precursors are fragmented across their full chromatographic elution profile. This is in contrast to DDA-based MS/MS where serial selection of precursor ions is biased toward interrogation and detection of the highest abundance sample components by virtue of the intensity-driven interrogation scheme employed. Both modes of acquisition were applied to a simple four-protein standard mixture with a 16-fold dynamic range in concentration, an in-gel digest of the Arabidopsis thaliana protein FLS2 purified by immunoprecipitation, and a solution-digested tomato leaf proteome sample. Dramatic improvement for individual protein sequence coverage was obtained for all three samples analyzed by the DIA approach, particularly for the lowest abundance sample components. In many instances, precursors readily detected and identified during DIA were either interrogated by MS/MS during DDA at inopportune points in their chromatographic elution profiles resulting in poor quality product ion spectra or not interrogated at all. Detailed evaluation of both DDA and DIA raw data and timing of the MS-to-MS/MS switching events clearly revealed the fundamental limitations of serial MS/MS interrogation and the advantages of parallel fragmentation by DIA for more comprehensive protein identification and characterization which holds promise for enhanced isoform and post-translational modification analysis.}, number={7}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Blackburn, Kevin and Mbeunkui, Flaubert and Mitra, Srijeet K. and Mentzel, Tobias and Goshe, Michael B.}, year={2010}, month={Jul}, pages={3621–3637} }
 @article{mitra_walters_clouse_goshe_2009, title={An Efficient Organic Solvent Based Extraction Method for the Proteomic Analysis of Arabidopsis Plasma Membranes}, volume={8}, ISSN={["1535-3907"]}, DOI={10.1021/pr801044y}, abstractNote={Membrane proteins are involved in diverse cellular processes and are an integral component of many signaling cascades, but due to their highly hydrophobic nature and the complexities associated with studying these proteins in planta, alternative methods are being developed to better characterize these proteins on a proteome-wide scale. In our previous work ( Mitra , S. K. et al. J. Proteome Res. 2007 , 6 , ( 5 ), 1933 - 50 ), methanol-assisted solubilization was determined to facilitate the identification of both hydrophobic and hydrophilic membrane proteins compared to Brij-58 solubilization and was particularly effective for leucine-rich repeat receptor-like kinases (LRR RLKs). To improve peptide identification and to overcome sample losses after tryptic digestion, we have developed an effective chloroform extraction method to promote plasma membrane protein identification. The use of chloroform extraction over traditional solid-phase extraction (SPE) prior to off-line strong cation exchange liquid chromatography (SCXC) and reversed-phase liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis facilitated the removal of chlorophylls, major contaminants of plant tissue preparations that can affect downstream analysis, in addition to the effective removal of trypsin used in the digestion. On the basis of a statistically derived 5% false discovery rate, the chloroform extraction procedure increased the identification of unique peptides for plasma membrane proteins over SPE by 70% which produced nearly a 2-fold increase in detection of membrane transporters and LRR RLKs without increased identification of contaminating Rubisco and ribosomal peptides. Overall, the combined use of methanol and chloroform provides an effective method to study membrane proteins and can be readily applied to other tissues and cells types for proteomic analysis.}, number={6}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Mitra, Srijeet K. and Walters, Benjamin T. and Clouse, Steven D. and Goshe, Michael B.}, year={2009}, month={Jun}, pages={2752–2767} }
 @article{mitra_gantt_ruby_clouse_goshe_2007, title={Membrane proteomic analysis of Arabidopsis thaliana using alternative solubilization techniques}, volume={6}, ISSN={["1535-3907"]}, DOI={10.1021/pr060525b}, abstractNote={This study presents a comparative proteomic analysis of the membrane subproteome of whole Arabidopsis seedlings using 2% Brij-58 or 60% methanol to enrich and solubilize membrane proteins for strong cation exchange fractionation and reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 441 proteins were identified by our Brij-58 method, and 300 proteins were detected by our methanol-based solubilization approach. Although the total number of proteins obtained using the nonionic detergent was higher than the total obtained by organic solvent, the ratio of predicted membrane proteins to total proteins identified indicates up to an 18.6% greater enrichment efficiency using methanol. Using two different bioinformatics approaches, between 31.0 and 40.0% of the total proteins identified by the methanol-based method were classified as containing at least one putative transmembrane domain as compared to 22.0-23.4% for Brij-58. In terms of protein hydrophobicity as determined by the GRAVY index, it was revealed that methanol was more effective than Brij-58 for solubilizing membrane proteins ranging from -0.4 (hydrophilic) to +0.4 (hydrophobic). Methanol was also approximately 3-fold more effective than Brij-58 in identifying leucine-rich repeat receptor-like kinases. The ability of methanol to effectively solubilize and denature both hydrophobic and hydrophilic proteins was demonstrated using bacteriorhodopsin and cytochrome c, respectively, where both proteins were identified with at least 82% sequence coverage from a single reversed-phase LC-MS/MS analysis. Overall, our data show that methanol is a better alternative for identifying a wider range of membrane proteins than the nonionic detergent Brij-58.}, number={5}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Mitra, Srijeet K. and Gantt, John A. and Ruby, James F. and Clouse, Steven D. and Goshe, Michael B.}, year={2007}, pages={1933–1950} }