Allis Chien

All Publications

• Enhancing Data Reliability in TOMAHAQ for Large-Scale Protein Quantification. Proteomics Liu, F., Singhal, K., Matney, R., Acharya, S., Akdis, C. A., Nadeau, K. C., Chien, A. S., Leib, R. D. 2020: e1900105

  Abstract

  The analytical scale of most mass spectrometry (MS)-based targeted proteomics assays is usually limited by assay performance and instrument utilization. A recently introduced method, called Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ), combines both peptide and sample multiplexing to simultaneously improve analytical scale and quantitative performance. In the present work we discuss critical technical requirements and data analysis considerations for successful implementation of the TOMAHAQ technique based on our study of a total of 185 target peptides across over 200 clinical plasma samples. Importantly, we observed significant interference originating from the TMTzero reporter ion used for the synthetic trigger peptides. This interference is not expected because only TMT10plex reporter ions from the target peptides should be observed under typical TOMAHAQ conditions. In order to unlock the great promise of the technique for high throughput quantification, here we propose a post-acquisition data correction strategy to deconvolute the reporter ion superposition and recover reliable data. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1002/pmic.201900105

  View details for PubMedID 32032464

• ABRF-sPRG 2018-2019: Development and Characterization of a Stable-Isotope Labeled Phosphopeptide Standard. Journal of biomolecular techniques : JBT Herren, A., Searle, B., Hawke, D., Lee, K., Koller, A., Leib, R., Phinney, B., Chien, A., Patel, B. 2019; 30 (Suppl): S2–S3

  Abstract

  The mission of the ABRF Proteomics Standards Research Group (sPRG) is to identify and implement technical standards that reflect the ABRF's commitment to accuracy, clarity, and consistency in the field of proteomics. There is broad interest in quantifying protein phosphorylation alterations in cellular signaling pathways under different conditions. The transient nature and low abundance of many phosphorylation sites makes this analysis challenging. Here we report on the follow up of the two-year sPRG study designed to target various issues encountered in phosphopeptide experiments. We have constructed a pool of heavy-labeled phosphopeptides that will enable core facilities to rapidly develop assays. Our pool contains over 150 phosphopeptides that have been previously observed in mass spectrometry data sets. The specific peptides have been chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling pathways: AMPK, death and apoptosis, ErbB, insulin/IGF-1, mTOR, PI3K/AKT, and stress (p38/SAPK/JNK). We feel this pool will enable researchers to test the effectiveness of their enrichment workflows and to provide a benchmark for a cross lab study. This standard should be helpful in number of ways, including providing a complete workflow solution for phosphopeptide enrichment, as an internal enrichment and chromatography calibrant, and as a pre-built biological assay for a wide variety of signaling pathways. Previously, we mixed the standard into an activated HeLa tryptic digest and distributed the mixture to over 60 ABRF member and nonmember laboratories around the world. We asked participants to enrich phosphopeptides out of the HeLa background and report ratios of the heavy phosphopeptides to the endogenous levels. In the current study, we continue validation of the standard within various RG group/ABRF members' laboratories. The aim of this follow up study is to provide reagents, an optimized phosphopeptide enrichment protocol, instrument acquisition method parameters, and data analysis templates.

  View details for PubMedID 31885518

• Impact of Enrichment Strategy on Observed Expression in Fresh Frozen Tissues. Journal of biomolecular techniques : JBT Singhal, K., Matney, R., Liu, F., Chien, A., Leib, R. 2019; 30 (Suppl): S21

  Abstract

  Human tissues obtained during clinical and surgical procedures are an invaluable resource for determining diagnosis, treatment response, and disease progression. In many cases, these biological specimens are preserved for future analyses, most commonly by formaldehyde fixation and paraffin embedding (FFPE). FFPE has the advantage that such specimens are stable at room temperature for years, but introduces additional complexity in terms of sample preparation, protein modifications or degradation. Frozen tissues are costly to store, but are preferred for post translational modification analyses even though they suffer some degradation on long timescales. Significant interest remains in optimizing recovery from both storage and sample processing conditions for these precious specimens. Here, we compare fresh frozen samples of different biological origin and complexity, such as heart, brain and lung tissues, and assess the differences between peptides enriched by hydrophilic interaction chromatography (HILIC) bound to MagReSyn polymer particles as compared to standard reversed phase C18 enrichment. For example, we lysed and extracted proteins from ~18mg of frozen normal autopsy heart tissue, digested with Trypsin/LysC and analyzed them using Orbitrap mass spectrometry. From a 500ng injection, we observed 1,749 proteins from C18 prep and 1,678 proteins from HILIC prep with 20k peptide spectrum matches in both cases. The proteins identified from both preparations are broadly similar in terms of protein families and function. But with more detailed analysis of the particular proteins and pathways observed, such as through tools like GeneTrail2, we observe each preparation prefers particular pathway members. Here, HILIC preparation favors identification of proteins involved in glycolysis while C18 preparation identified proteins involved in GTP hydrolysis and ribosomal assembly. We will further analyze additional tissues, including lung tissue with adenocarcinoma and brain tissue with glioblastoma, with an eye to understanding the advantages or disadvantages of particular preparations based on the biological hypothesis being tested.

  View details for PubMedID 31892888

• Data Independent Acquisition in Practice: Foundations and Resources for Implementing DIA. Journal of biomolecular techniques : JBT Neely, B., Kirkpatrick, J., Midha, M., Stemmer, P., Martin, L., Wang, Y., Herring, L., Phinney, B., Shan, B., Chien, A., Jagtap, P. 2019; 30 (Suppl): S46

  Abstract

  Proteomics researchers are realizing the promise of Data-Independent Acquisition (DIA). In its 2017/2018 study, the ABRF Proteomics Research Group (PRG) have conducted a worldwide study to offer a go-to resource for sample processing, data acquisition and data analysis for new users interested in DIA studies. This workshop will facilitate an in-depth discussion of the PRG study results, and provide practical demonstrations utilizing those created during the PRG study. Workshop Goals: Educate and provide online educational resources for DIA that aid in the areas of sample preparation, data acquisition, data analysis and interpretation; enable academic and core facilities to use DIA technology by providing expert insights and possible improvements to existing workflows; share experience with attendees on some common lessons learnt during the PRG study; and lay the foundation for attendees to implement DIA at their own institution.

  View details for PubMedID 31896981

  View details for PubMedCentralID PMC6938267

• 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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  View details for Web of Science ID 000165337800008

• 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

  View details for Web of Science ID 000071624500025