Mass Spectrometry Facility

Facility Tabs

Overview

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, and an OpenSPR 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 any questions, please contact the director of mass spectrometry facility, Shouling Xu, 650-739-4225, or via email, sxu@ciw.edu.

Research

Xu group is currently focusing on :1) method development on XL-MS for structrual analysis of complex protein assembly, such as splicing complex and photosynthesis apparatus; 2) improvement on enrichment and detection of sugar-modified and lysine-methylated proteins in plants; 3) functional studies of the PTM,esp. O-GlcNAcylation, on proteins in plants. 4) Cell altas using crosslinking mass spectrometry and proximity labeling mass spectrometry.

Postdoc position available. Please email me if you are interested!

Funding resources: NIH R01, Carnegie Endowment and Venture grant.

Resources

Easy-nLC1200 System

Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer

ÄKTA pure 25 M System

ÄKTApurifier 10

OpenSPR

Facility Manager

Shouling Xu

Research Scientist

Plant Biology

Carnegie Institution for Science

sxu@carnegiescience.edu
650-739-4225
Office:
260 Panama Street
Stanford, CA 94305, US

Profile

Affiliation

Carnegie Affiliation:

DPB Employees

DPB Affiliation:

DPB Faculty

Labs:

Xu Lab

2017-present: Director of Proteomics Facility, Carnegie Institution at Stanford

2017-present: Research Scientist / PI, Carnegie Institution at Stanford

2008, Ph.D, University of North Carolina at Chapel Hill

Teaching

Websites

Stanford Links

Xu lab

Facility website

Carnegie Mass Spectrometry Facility

Personnel

Su Hong (Research Associate)
I am a chemist by training. I have graduated from Imperial College London with BSc and ARCS in Chemistry (First Class honours), completed Master’s degree in Chemistry at Seoul National University in Korea, and earned my PhD degree in Chemistry from Stanford University. My PhD research focused on “Bioinspired Melanin Nanoparticles for Multimodality Imaging and Biocatalysis."

I joined Xu lab at Carnegie Institution for Science in February, 2019.
Danbi Byun (Research Assistant)
I graduated from UC Davis with B.S. degree in Biotechnology with Outstanding Undergraduate Accomplishment Award from the Plant Sciences Department. I joined the Xu lab in January 2019. My research direction is adapting proteomic tools to study molecular machineries and cell atlas in plants. Before I joined Carnegie, I interned at a neurophysiology lab in UC Davis and worked at several dental offices as a predental student. In my freetime, I enjoy making pottery, traveling, and watching animal videos.
Malika Kaderali (Research Assistant)
I graduated from University of California, Berkeley with two degrees in Integrative Biology and Sociology at. I have been working as a medical assistant, which deals with direct patient care and preparing blood, saliva, culture, and urine specimens for further analysis. In efforts to further delve into learning more about proteomics, I joined the Xu lab in October 2019. Outside of working in the science field, I enjoy trying new foods, traveling, and playing basketball.

Senior Users

Chuan-Chih Hsu (Postdoctoral Fellow)
I am from Taichung City, Taiwan. I obtained a BS in Agricultural Chemistry from National Taiwan University in Taipei City, Taiwan in June 2007. I then decided to study analytical chemistry so I spent two years to complete a MS in Chemistry at National Taiwan University with Dr. Yu-Ju Chen as my advisor in June 2009. I then moved to West Lafayette in Auguest 2012, and I joined Dr. Andy Tao's lab and spent time designing novel (phospho)proteomic strategies toward comprehensive phosphoproteomic analysis. I recieved my PhD degree in Biochemistry from Purdue University in September 2017, and I joined Dr. Wang's lab as a postdoc in June 2018. I am interested in the development of novel mass spectrometry(MS)-based approaches that faciliate systematically analysis of plant signal transduction and proteome perturbation in response to extracellular stimuli. I believe that MS is a cutting-edge technique to identify all the proteins involved in various biological processes and to illustrate their functional mechanisms in plant cells. My current research project focuses on the study of phosphorylation events in plants under environmental stresses. In my spare time, I enjoy jogging, watching movie, and listening to classical music.

Publications

Selected Publications

Park CH, Youn JH, Xu SL, Kim JG, Bi Y, Xu N, Mudgett SK, Kim TW, Wang ZY. BSUI family phosphatases mediate Flagellin-FLS2 signaling through a specific phosphocode. 2019. bioRxiv. doi: https://doi.org/10.1101/685610.

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. 2020. Plant Cell. doi: DOI: https://doi.org/10.1105/tpc.20.00044.

Zhao JL, Zhang N, Liu LQ, Xu SL, Yue ZL, Zhang LL, Deng Z, Burlingame AL, Su DY, Wang ZY, Sun Y, Zhang SW. Mutual Regulation of receptor-like kinase SIT and B'k-PP2A shapes the early response of rice to salt stress. 2019. Plant Cell. DOI: https://doi.org/10.1105/tpc.18.00706

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 . doi: https://doi.org/10.1101/636324

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. doi: https://doi.org/10.1101/629675. eLIFE. DOI: 10.7554/eLife.47864

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. DOI: https://doi.org/10.1105/tpc.18.00941

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), Highlighted in F1000; Spotlighted by Zhu & Huq, 2014.

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]

News

Congratulations! Our collaborator Callie Wiginton's paper from Cyert lab on Calcineurin network is in press in Molecular Cell! https://www.cell.com/molecular-cell/fulltext/S1097-2765(20)30431-7

Congratulations! Our collaborator Veder Garcia's paper from Wang lab on TRIPP has been published in Plant Cell! http://www.plantcell.org/content/early/2020/05/05/tpc.20.00044

Nov 2019, Xu lab received 5-year NIH R01 award on project: " Nutrient regulation of alternative splicing and Transcription by O-GlcNAcylation".

Sep 2019, Congratulations! Our collaborator Andrea Mair's paper from Dominique Bergmann lab on TurboID in plants has been published in eLife. https://elifesciences.org/articles/47864

Protocols

In gel digestion for mass spectrometric analysis

IP-MS

Enrichment of Biotinylated proteins from plants using TurboID transgenic lines

Enrichment of Biotinylated peptides from plants using TurboID transgenic lines

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