Mass Spectrometry Facility

Introduction

The Carnegie mass spectrometry facility adapts and develops proteomic tools to drive biological studies. The facility is in close collaboration with various groups at Carnegie and labs at Stanford biology department.

The facility includes one benchtop quadrupole Orbitrap mass spectrometer (Q-Exactive HF) coupled with nano-flow UHPLC liquid chromatography (Thermo Scientific Easy-nLC 1200 system). The facility is also equipped with AKTA purifier 10 and pure 25 M chromatography system.

The facility provides analysis for identification of both proteins and post-translation modifications, including phosphorylation, ubiquitination, methylation and O-GlcNAcylation. The facility is also providing cross-linking analysis for mapping protein structure of functional protein complexes. For quantification, the facility provides both MS1 based quantification (spectra count and label-free quantification-LFQ, SILAC-based N15 metabolic labeling) and MS2-based quantification (Parallel Reaction monitoring-PRM). Tools used by Carnegie mass spectrometry facility for analysis of large mass spectrometry proteomics data include Protein Prospector, MaxQuant, Perseus and Skyline. An internal Carnegie server is set up for deposition and processing of MS data.

For questions, please contact the proteomic director Shouling Xu, sxu@carnegiescience.edu, 650-739-4225.

Personnel

Shouling Xu
Director of Proteomics, PI
Cell mapping, structural analysis using cross-linking mass spectrometry, nutrient sensing
Office: 650-739-4225
Email: sxu@carnegeiscience.edu

Su Hyun Hong
Research Associate
Email: shong@carnegiescience.edu

Danbi Byun 
Research Assistant
Study area: nutrient sensing ; structural analysis using cross-linking mass spectrometry;  
Email:dbyun@carnegiescience.edu

Rick Kim
Joint Research Associate, Grossman Lab and Xu Lab
Area: Study of lysine methylation in Clamy

Senior Users

Weimin Ni
Postdoctoral Scholar, Grossman Lab
LC-MS analysis of regulatory proteins and protein complexes
Email: wni@carnegiescience.edu
Expertise: 
Calibration and Maintenance of HPLC and MS instrument; Data analysis using Protein Prospector and Maxquant; PRM set up and data analysis using Skyline; Quantitative Mass Spectrometry analysis using Metabolic labeling and LFQ; Post-translational modifications analysis, HPLC (AKTA) –Reverse HPLC, Ion Exchange and Size Exclusion Chromatography, Sample prep from various tissues.

Chuan-Chih Hsu
Postdoctoral Associate, Wang Lab
Study of phosphorylation events in plants under environmental stresses
Expertise: Skilled user of HPLC and MS instrument; Data analysis using Protein Prospector and Maxquant; Quantitative Mass Spectrometry analysis using LFQ; Post-translational modifications analysis; Sample prep method development.   

Selected Publications

Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC. Proximity labeling of protein complexes and cell-type specific organellar proteomes in Arabidopsis enabled by TurboID. 2019. BioRxiv (under review of eLife).  doi: https://doi.org/10.1101/629675. 

Kim TW, Park CH, Hsu CC, Zhu JY, Hsiao Y, Branon TC, Xu SL, Ting AY, Wang ZY. Application of TurboID-mediated proximity labeling for mapping a GSK3 kinase signaling network in Arabidopsis. 2019. BioRxiv (under review of eLife). 

Garcia VJ, Xu SL, Raksha R, Wang W, Elliott L, Fensenko M, Altmann M, Falter-Braun, P, Moore I, Assadd FF, Wang ZY. Proteomic Studies of the Arabidopsis TRAPP complexes reveal conserved organization and a novel plant-specific component with a role in plant development. 2019. (under review of Plant Cell). 

Kim EJ, Lee SH, Park CH, Kim SH, Hsu CC, Xu S, Wang Z, Kim SK, Kim TW. Plant U-Box 40 Mediates Degradation of the Brassinosteroid-Responsive Transcription Factor BZR1 in Arabidopsis Roots. Plant CELL. 2019. 

Xu SL, Chalkley JR, Maynard JC, Wang W, Ni W, Jiang XY, Shin K, Cheng L, Savage D, Huhmer AFR, Burlingame AL, and Wang ZY. 2017. Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis. PNAS, 114, E1536–E1543. [ PubMed]

Ni W*, Xu SL*, Grandio EG, Chalkley RJ, Huhmer AF, Burlingame AL , Wang ZY and Quail PH . 2017. PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat Commun , 8, 15236. [PubMed] Highlighted in F1000.

Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ. 2016.N-Glycopeptide profiling in Arabidopsis inflorescence.MCP. 15(6), 2048-2054. [ PubMed].

Ni W *, Xu SL *, Tepperman JM, Stanley DJ, Maltby DA , Gross JD, Burlingame AL , Wang ZY and Quail PH . 2014. A mutually assured destruction mechanism attenuates light signaling in Arabidopsis. Science , 344, 1160-64. [ PubMed] Highlighted by Hines (2014), Emerging from the shade into the light, Sci Signal. 7 (329): ec161, 2014; Highlighted in F1000; Spotlighted by Zhu & Huq, 2014, Suicidal codegradation of the Phytochrome Interacting Factor 3 and phytochrome B in response to light. Mol. Plant, doi:10.1093/mp/ssu108.

Kim EJ, Youn JH, Park CH, Kim TW, Guan S, Xu S, Burlingame AL, Kim YP, Kim SK, Wang ZY, Kim TW. 2016. Oligomerization between BSU1 Family Members Potentiates Brassinosteroid Signaling in Arabidopsis. Mol Plant , 9(1): 178-181. [ PubMed]

Xu P*, Xu SL*, Li ZJ, Tang W, Burlingame AL, Wang ZY. 2014. A brassinosteroid-signaling kinase interacts with multiple receptor-like kinases in Arabidopsis. Mol Plant , 7(2):441-4. [ PubMed]

Ni W *, Xu SL *, Chalkley RJ , Pham TN , Guan S , Maltby DA , Burlingame AL , Wang ZY and Quail PH . 2013. Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback-modulation of photoreceptor phyB levels in Arabidopsis. Plant Cell, 25: 2679-98. [ PubMed]