Current Role at Stanford

Director, Stanford University Mass Spectrometry (SUMS) core resource laboratory

Institute Affiliations

Education & Certifications

  • PhD, Stanford University, Chemistry (2000)
  • BS, University of San Francisco, Chemistry, Biochemistry (1994)


Professional Affiliations and Activities

  • Executive Board, Association of Biomolecular Resource Facilities (ABRF) (2015 - 2019)
  • Coordinator, ASMS Analytical Lab Managers Interest Group (2015 - 2017)
  • Member, ABRF (2000 - Present)
  • Member, American Society for Mass Spectrometry (ASMS) (2000 - Present)
  • Member, American Chemical Society (ACS) (1992 - Present)


All Publications

  • Identification of widespread antibiotic exposure in cholera patients correlates with clinically relevant microbiota changes. The Journal of infectious diseases Alexandrova, L., Haque, F., Rodriguez, P., Marrazzo, A. C., Grembi, J. A., Ramachandran, V., Hryckowian, A. J., Adams, C. M., Siddique, M. S., Khan, A. I., Qadri, F., Andrews, J. R., Rahman, M., Spormann, A. M., Schoolnik, G. K., Chien, A., Nelson, E. J. 2019


    A first step to combating antimicrobial resistance in enteric pathogens is to establish an objective assessment of antibiotic exposure. Our goal was to develop and evaluate a liquid chromatography-ion trap mass spectrometry (LC/MS) method to determine antibiotic exposure in cholera patients.A priority list for targeted LC/MS was generated from medication vendor surveys in Bangladesh. A study of cholera and non-cholera patients was conducted to collect and analyze paired urine and stool samples.Among 845 patients, 11% (n=90) were Vibrio cholerae positive; at least one antibiotic was detected in 86% and at least two in 52% of cholera stools. Among paired urine and stool (n=44), at least one antibiotic was detected in 98% and at least two in 84%, despite 55% self-reporting medication use. Compared to LC/MS, a low-cost antimicrobial detection bio-assay lacked sufficient negative predictive value (10%; 95% CI 6-16). Detection of guideline-recommended antibiotics in stool did (azithromycin; p=0.040) and did not (ciprofloxacin) correlate with V. cholerae suppression. A non-recommended antibiotic (metronidazole) was associated with decreases in anaerobes (Prevotella; p<0.001).The findings suggest there may be no true negative control group when attempting to account for antibiotic exposure in settings like those in this study.

    View details for DOI 10.1093/infdis/jiz299

    View details for PubMedID 31192364

  • Plasma anandamide concentrations are lower in children with autism spectrum disorder MOLECULAR AUTISM Karhson, D. S., Krasinska, K. M., Dallaire, J., Libove, R. A., Phillips, J. M., Chien, A. S., Garner, J. P., Hardan, A. Y., Parker, K. J. 2018; 9: 18


    Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by restricted, stereotyped behaviors and impairments in social communication. Although the underlying biological mechanisms of ASD remain poorly understood, recent preclinical research has implicated the endogenous cannabinoid (or endocannabinoid), anandamide, as a significant neuromodulator in rodent models of ASD. Despite this promising preclinical evidence, no clinical studies to date have tested whether endocannabinoids are dysregulated in individuals with ASD. Here, we addressed this critical gap in knowledge by optimizing liquid chromatography-tandem mass spectrometry methodology to quantitatively analyze anandamide concentrations in banked blood samples collected from a cohort of children with and without ASD (N = 112).Anandamide concentrations significantly differentiated ASD cases (N = 59) from controls (N = 53), such that children with lower anandamide concentrations were more likely to have ASD (p = 0.041). In keeping with this notion, anandamide concentrations were also significantly lower in ASD compared to control children (p = 0.034).These findings are the first empirical human data to translate preclinical rodent findings to confirm a link between plasma anandamide concentrations in children with ASD. Although preliminary, these data suggest that impaired anandamide signaling may be involved in the pathophysiology of ASD.

    View details for PubMedID 29564080

  • Proteomics of Primary Cilia by Proximity Labeling DEVELOPMENTAL CELL Mick, D. U., Rodrigues, R. B., Leib, R. D., Adams, C. M., Chien, A. S., Gygi, S. P., Nachury, M. V. 2015; 35 (4): 497-512


    While cilia are recognized as important signaling organelles, the extent of ciliary functions remains unknown because of difficulties in cataloguing proteins from mammalian primary cilia. We present a method that readily captures rapid snapshots of the ciliary proteome by selectively biotinylating ciliary proteins using a cilia-targeted proximity labeling enzyme (cilia-APEX). Besides identifying known ciliary proteins, cilia-APEX uncovered several ciliary signaling molecules. The kinases PKA, AMPK, and LKB1 were validated as bona fide ciliary proteins and PKA was found to regulate Hedgehog signaling in primary cilia. Furthermore, proteomics profiling of Ift27/Bbs19 mutant cilia correctly detected BBSome accumulation inside Ift27(-/-) cilia and revealed that β-arrestin 2 and the viral receptor CAR are candidate cargoes of the BBSome. This work demonstrates that proximity labeling can be applied to proteomics of non-membrane-enclosed organelles and suggests that proteomics profiling of cilia will enable a rapid and powerful characterization of ciliopathies.

    View details for DOI 10.1016/j.devcel.2015.10.015

    View details for Web of Science ID 000365099300013

    View details for PubMedID 26585297

    View details for PubMedCentralID PMC4662609

  • Neural Precursor Cell-expressed Developmentally Down-regulated Protein 4-2 (Nedd4-2) Regulation by 14-3-3 Protein Binding at Canonical Serum and Glucocorticoid Kinase 1 (SGK1) Phosphorylation Sites JOURNAL OF BIOLOGICAL CHEMISTRY Chandran, S., Li, H., Dong, W., Krasinska, K., Adams, C., Alexandrova, L., Chien, A., Hallows, K. R., Bhalla, V. 2011; 286 (43): 37830-37840


    Regulation of epithelial Na(+) channel (ENaC)-mediated transport in the distal nephron is a critical determinant of blood pressure in humans. Aldosterone via serum and glucocorticoid kinase 1 (SGK1) stimulates ENaC by phosphorylation of the E3 ubiquitin ligase Nedd4-2, which induces interaction with 14-3-3 proteins. However, the mechanisms of SGK1- and 14-3-3-mediated regulation of Nedd4-2 are unclear. There are three canonical SGK1 target sites on Nedd4-2 that overlap phosphorylation-dependent 14-3-3 interaction motifs. Two of these are termed "minor," and one is termed "major," based on weak or strong binding to 14-3-3 proteins, respectively. By mass spectrometry, we found that aldosterone significantly stimulates phosphorylation of a minor, relative to the major, 14-3-3 binding site on Nedd4-2. Phosphorylation-deficient minor site Nedd4-2 mutants bound less 14-3-3 than did wild-type (WT) Nedd4-2, and minor site Nedd4-2 mutations were sufficient to inhibit SGK1 stimulation of ENaC cell surface expression. As measured by pulse-chase and cycloheximide chase assays, a major binding site Nedd4-2 mutant had a shorter cellular half-life than WT Nedd4-2, but this property was not dependent on binding to 14-3-3. Additionally, a dimerization-deficient 14-3-3ε mutant failed to bind Nedd4-2. We conclude that whereas phosphorylation at the Nedd4-2 major site is important for interaction with 14-3-3 dimers, minor site phosphorylation by SGK1 may be the relevant molecular switch that stabilizes Nedd4-2 interaction with 14-3-3 and thus promotes ENaC cell surface expression. We also propose that major site phosphorylation promotes cellular Nedd4-2 protein stability, which potentially represents a novel form of regulation for turnover of E3 ubiquitin ligases.

    View details for DOI 10.1074/jbc.M111.293233

    View details for Web of Science ID 000296542400077

    View details for PubMedID 21900244

    View details for PubMedCentralID PMC3199524

  • The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses PROTEOMICS Friedman, D. B., Andacht, T. M., Bunger, M. K., Chien, A. S., Hawke, D. H., Krijgsveld, J., Lane, W. S., Lilley, K. S., MacCoss, M. J., Moritz, R. L., Settlage, R. E., Sherman, N. E., Weintraub, S. T., Witkowska, H. E., Yates, N. A., Turck, C. W. 2011; 11 (8): 1371-1381


    Resource (core) facilities have played an ever-increasing role in furnishing the scientific community with specialized instrumentation and expertise for proteomics experiments in a cost-effective manner. The Proteomics Research Group (PRG) of the Association of Biomolecular Resource Facilities (ABRF) has sponsored a number of research studies designed to enable participants to try new techniques and assess their capabilities relative to other laboratories analyzing the same samples. Presented here are results from three PRG studies representing different samples that are typically analyzed in a core facility, ranging from simple protein identification to targeted analyses, and include intentional challenges to reflect realistic studies. The PRG2008 study compares different strategies for the qualitative characterization of proteins, particularly the utility of complementary methods for characterizing truncated protein forms. The use of different approaches for determining quantitative differences for several target proteins in human plasma was the focus of the PRG2009 study. The PRG2010 study explored different methods for determining specific constituents while identifying unforeseen problems that could account for unanticipated results associated with the different samples, and included (15) N-labeled proteins as an additional challenge. These studies provide a valuable educational resource to research laboratories and core facilities, as well as a mechanism for establishing good laboratory practices.

    View details for DOI 10.1002/pmic.201000736

    View details for Web of Science ID 000289528800001

    View details for PubMedID 21394914

  • Detecting Reaction Intermediates in Liquids on the Millisecond Time Scale Using Desorption Electrospray Ionization ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Perry, R. H., Splendore, M., Chien, A., Davis, N. K., Zare, R. N. 2011; 50 (1): 250-254

    View details for DOI 10.1002/anie.201004861

    View details for Web of Science ID 000285891900019

    View details for PubMedID 21110361

  • Azetidine-2-carboxylic acid in the food chain PHYTOCHEMISTRY Rubenstein, E., McLaughlin, T., Winant, R. C., Sanchez, A., Eckart, M., Krasinska, K. M., Chien, A. 2009; 70 (1): 100-104


    Azetidine-2-carboxylic acid (Aze) 1 is a non-protein amino acid present in sugar beets and in table beets (Beta vulgaris). It is readily misincorporated into proteins in place of proline 2 in many species, including humans, and causes numerous toxic effects as well as congenital malformations. Its role in the pathogenesis of disease in humans has remained unexplored. Sugar beet agriculture, especially in the Northern Hemisphere, has become widespread during the past 150 years, and now accounts for nearly 30% of the world's supply of sucrose. Sugar beet byproducts are also used as a dietary supplement for livestock. Therefore, this study was undertaken as an initial survey to identify Aze-containing links in the food chain. Herein, we report the presence of Aze 1 in three sugar beet byproducts that are fed to farm animals: sugar beet molasses, shredded sugar beet pulp, and pelleted sugar beet pulp.

    View details for DOI 10.1016/j.phytochem.2008.11.007

    View details for Web of Science ID 000264235800012

    View details for PubMedID 19101705

  • Azetidine-2-carboxylic acid in garden beets (Beta vulgaris) PHYTOCHEMISTRY Rubenstein, E., Zhou, H., Krasinska, K. M., Chien, A., Becker, C. H. 2006; 67 (9): 898-903


    Azetidine-2-carboxylic acid (L-Aze) is a toxic and teratogenic non-protein amino acid. In many species, including man, L-Aze is misincorporated into protein in place of proline, altering collagen, keratin, hemoglobin, and protein folding. In animal models of teratogenesis, it causes a wide range of malformations. The role of L-Aze in human disease has been unexplored, probably because the compound has not been associated with foods consumed by humans. Herein we report the presence of L-Aze in the garden or table beet (Beta vulgaris).

    View details for DOI 10.1016/j.phytochem.2006.01.028

    View details for Web of Science ID 000237600300009

    View details for PubMedID 16516254

  • A double-vented tetraphasic continuous column approach to MuDPIT analysis on long capillary columns demonstrates superior proteomic coverage JOURNAL OF PROTEOME RESEARCH Guzzetta, A. W., Chien, A. S. 2005; 4 (6): 2412-2419


    A double-vented serial tetraphasic capillary column approach is applied to proteomic MuDPIT-type analysis using extended length capillary reverse-phase columns. The heart of the tetraphasic device consists of a triphasic MuDPIT trap located upstream of a venting tee. The trap is followed by a 60 cm high-resolution capillary column. A conventional high-flow HPLC is used to develop gradients at standard flow rates and pressures. The double-vented triphasic MuDPIT trapping device relieves the capillary separation column from the salt burden during the on-line cation-exchange portion of the analysis. Two configurations are presented, a double-vented continuous column model and a discontinuous model in which the triphasic MuDPIT trap is installed on a six-port valve; both configurations were tested with 60 and 10 cm capillary columns. All four systems were challenged with a trypsin digest of undepleted human serum, and a matrix of proteomic results for the different models and column lengths are compared.

    View details for DOI 10.1021/or050209h

    View details for Web of Science ID 000234007200062

    View details for PubMedID 16335995

  • Multiple active oxidants in cytochrome P-450 model oxidations JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Collman, J. P., Chien, A. S., Eberspacher, T. A., Brauman, J. I. 2000; 122 (45): 11098-11100
  • Competitive reaction of axial ligands during biomimetic oxygenations INORGANIC CHEMISTRY Collman, J. P., Chien, A. S., Eberspacher, T. A., Zhong, M., Brauman, J. I. 2000; 39 (20): 4625-4629

    View details for DOI 10.1021/ic000071z

    View details for Web of Science ID 000089707500034

  • An agostic alternative to the P-450 rebound mechanism JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Collman, J. P., Chien, A. S., Eberspacher, T. A., Brauman, J. I. 1998; 120 (2): 425-426