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Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BJM, Nakayasu ES, Qian WJ, Metz TO. Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements. Trends Mol Med 2024:S1471-4914(24)00195-3. [PMID: 39152082 DOI: 10.1016/j.molmed.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Type 1 diabetes (T1D) is a devastating autoimmune disease for which advanced mass spectrometry (MS) methods are increasingly used to identify new biomarkers and better understand underlying mechanisms. For example, integration of MS analysis and machine learning has identified multimolecular biomarker panels. In mechanistic studies, MS has contributed to the discovery of neoepitopes, and pathways involved in disease development and identifying therapeutic targets. However, challenges remain in understanding the role of tissue microenvironments, spatial heterogeneity, and environmental factors in disease pathogenesis. Recent advancements in MS, such as ultra-fast ion-mobility separations, and single-cell and spatial omics, can play a central role in addressing these challenges. Here, we review recent advancements in MS-based molecular measurements and their role in understanding T1D.
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Affiliation(s)
- Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yu Mi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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2
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Kim DH, Sung M, Park MS, Sun EG, Yoon S, Yoo KH, Radhakrishnan K, Jung SY, Bae WK, Cho SH, Chung IJ. Galectin 3-binding protein (LGALS3BP) depletion attenuates hepatic fibrosis by reducing transforming growth factor-β1 (TGF-β1) availability and inhibits hepatocarcinogenesis. Cancer Commun (Lond) 2024. [PMID: 39073023 DOI: 10.1002/cac2.12600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 07/04/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Increased Galectin 3-binding protein (LGALS3BP) serum levels have been used to assess hepatic fibrosis stages and the severity of hepatocellular carcinoma (HCC). Considering the crucial role of transforming growth factor-β1 (TGF-β1) in the emergence of these diseases, the present study tested the hypothesis that LGALS3BP regulates the TGF-β1 signaling pathway. METHODS The expression levels of LGALS3BP and TGFB1 were analyzed in patients with metabolic dysfunction-associated steatohepatitis (MASH) and HCC. Multiple omics techniques, such as RNA-sequencing, transposase-accessible chromatin-sequencing assay, and liquid chromatography-tandem mass spectrometry proteomics, were used to identify the regulatory mechanisms for the LGALS3BP-TGF-β1 axis. The effects of altered TGF-β1 signaling by LGALS3BP were investigated in conditional LGALS3BP-knockin and LGALS3BP-knockout mice. RESULTS In patients with MASH and HCC, the levels of LGALS3BP and TGFB1 exhibited positive correlations. Stimulation of LGALS3BP by the inflammatory cytokine interferon α in HCC cells or ectopic overexpression of LGALS3BP in hepatocytes promoted the expression levels of TGFB1. Aggravated fibrosis was observed in the livers of hepatocyte-specific LGALS3BP-knockin mice, with increased TGFB1 levels. LGALS3BP directly bound to and assembled integrin αV, an integral mediator required for releasing active TGF-β1 from extracellular latent complex with the rearranged F-actin cytoskeleton. The released TGF-β1 activated JunB transcription factor, which in turn promoted the TGF-β1 positive feedback loop. LGALS3BP deletion in the hepatocytes downregulated TGF-β1 signaling and CCl4 induced fibrosis. Moreover, LGALS3BP depletion hindered hepatocarcinogenesis by limiting the availability of fibrogenic TGF-β1. CONCLUSION LGALS3BP plays a crucial role in hepatic fibrosis and carcinogenesis by controlling the TGF-β1 signaling pathway, making it a promising therapeutic target in TGF-β1-related diseases.
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Affiliation(s)
- Dae-Hwan Kim
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Medical School, Hwasun, South Korea
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
- Combinatorial Tumor Immunotherapy MRC Center, Chonnam National University Medical School, Hwasun, South Korea
- National Immunotherapy Innovation Center, Hwasun, South Korea
| | - Minjeong Sung
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Medical School, Hwasun, South Korea
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
- Combinatorial Tumor Immunotherapy MRC Center, Chonnam National University Medical School, Hwasun, South Korea
- National Immunotherapy Innovation Center, Hwasun, South Korea
- BioMedical Sciences Graduate Program, Chonnam National University, Hwasun, South Korea
| | - Myong-Suk Park
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Medical School, Hwasun, South Korea
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
- Combinatorial Tumor Immunotherapy MRC Center, Chonnam National University Medical School, Hwasun, South Korea
- National Immunotherapy Innovation Center, Hwasun, South Korea
| | - Eun-Gene Sun
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Medical School, Hwasun, South Korea
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
- National Immunotherapy Innovation Center, Hwasun, South Korea
| | - Sumin Yoon
- Department of Biological Science, Sookmyung Women's University, Seoul, South Korea
| | - Kyung Hyun Yoo
- Department of Biological Science, Sookmyung Women's University, Seoul, South Korea
| | | | - Sung Yun Jung
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Woo-Kyun Bae
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Medical School, Hwasun, South Korea
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
- Combinatorial Tumor Immunotherapy MRC Center, Chonnam National University Medical School, Hwasun, South Korea
- National Immunotherapy Innovation Center, Hwasun, South Korea
- BioMedical Sciences Graduate Program, Chonnam National University, Hwasun, South Korea
| | - Sang-Hee Cho
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Medical School, Hwasun, South Korea
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
- Combinatorial Tumor Immunotherapy MRC Center, Chonnam National University Medical School, Hwasun, South Korea
- National Immunotherapy Innovation Center, Hwasun, South Korea
| | - Ik-Joo Chung
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Medical School, Hwasun, South Korea
- Department of Internal Medicine, Division of Hematology and Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
- Combinatorial Tumor Immunotherapy MRC Center, Chonnam National University Medical School, Hwasun, South Korea
- National Immunotherapy Innovation Center, Hwasun, South Korea
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Ross DH, Lee JY, Gao Y, Hollerbach AL, Bilbao A, Shi T, Ibrahim YM, Smith RD, Zheng X. Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-Based High-Resolution Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1539-1549. [PMID: 38864778 DOI: 10.1021/jasms.4c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Ion mobility spectrometry (IMS) is a gas-phase analytical technique that separates ions with different sizes and shapes and is compatible with mass spectrometry (MS) to provide an additional separation dimension. The rapid nature of the IMS separation combined with the high sensitivity of MS-based detection and the ability to derive structural information on analytes in the form of the property collision cross section (CCS) makes IMS particularly well-suited for characterizing complex samples in -omics applications. In such applications, the quality of CCS from IMS measurements is critical to confident annotation of the detected components in the complex -omics samples. However, most IMS instrumentation in mainstream use requires calibration to calculate CCS from measured arrival times, with the most notable exception being drift tube IMS measurements using multifield methods. The strategy for calibrating CCS values, particularly selection of appropriate calibrants, has important implications for CCS accuracy, reproducibility, and transferability between laboratories. The conventional approach to CCS calibration involves explicitly defining calibrants ahead of data acquisition and crucially relies upon availability of reference CCS values. In this work, we present a novel reference-free approach to CCS calibration which leverages trends among putatively identified features and computational CCS prediction to conduct calibrations post-data acquisition and without relying on explicitly defined calibrants. We demonstrated the utility of this reference-free CCS calibration strategy for proteomics application using high-resolution structures for lossless ion manipulations (SLIM)-based IMS-MS. We first validated the accuracy of CCS values using a set of synthetic peptides and then demonstrated using a complex peptide sample from cell lysate.
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Affiliation(s)
- Dylan H Ross
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jung Yun Lee
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yuqian Gao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Adam L Hollerbach
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aivett Bilbao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tujin Shi
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Yang L, Zhang Y, Hong X, Zhang K, Liu B, Zhang P, Tang Q, Yu J, Jin XZ, Jin XZ, Zhang N, Targher G, Byrne CD, Zhang Z, Zheng MH, Zhang J. Serum dithiothreitol-oxidizing capacity (DOC) is a promising biomarker for excluding significant liver fibrosis: a proof-of-concept study. BMC Med 2024; 22:278. [PMID: 38956533 PMCID: PMC11221035 DOI: 10.1186/s12916-024-03502-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND APRI and FIB-4 scores are used to exclude clinically significant fibrosis (defined as stage ≥ F2) in patients with chronic viral hepatitis. However, the cut-offs for these scores (generated by Youden indices) vary between different patient cohorts. This study aimed to evaluate whether serum dithiothreitol-oxidizing capacity (DOC), i.e., a surrogate test of quiescin sulfhydryl oxidase-1, which is a matrix remodeling enzyme, could be used to non-invasively identify significant fibrosis in patients with various chronic liver diseases (CLDs). METHODS Diagnostic performance of DOC was compared with APRI and FIB-4 for identifying significant fibrosis. ROC curve analyses were undertaken in: a) two chronic hepatitis B (CHB) cohorts, independently established from hospitals in Wenzhou (n = 208) and Hefei (n = 120); b) a MASLD cohort from Wenzhou hospital (n = 122); and c) a cohort with multiple CLD etiologies (except CHB and MASLD; n = 102), which was identified from patients in both hospitals. Cut-offs were calculated using the Youden index. All CLD patients (n = 552) were then stratified by age for ROC curve analyses and cut-off calculations. RESULTS Stratified by CLD etiology or age, ROC curve analyses consistently showed that the DOC test was superior to APRI and FIB-4 for discriminating between clinically significant fibrosis and no fibrosis, when APRI and FIB-4 showed poor/modest diagnostic performance (P < 0.05, P < 0.01 and P < 0.001 in 3, 1 and 3 cohort comparisons, respectively). Conversely, the DOC test was equivalent to APRI and FIB-4 when all tests showed moderate/adequate diagnostic performances (P > 0.05 in 11 cohort comparisons). DOC had a significant advantage over APRI or FIB-4 scores for establishing a uniform cut-off independently of age and CLD etiology (coefficients of variation of DOC, APRI and FIB-4 cut-offs were 1.7%, 22.9% and 47.6% in cohorts stratified by CLD etiology, 2.0%, 26.7% and 29.5% in cohorts stratified by age, respectively). The uniform cut-off was 2.13, yielded from all patients examined. Surprisingly, the uniform cut-off was the same as the DOC upper limit of normal with a specificity of 99%, estimated from 275 healthy control individuals. Hence, the uniform cut-off should possess a high negative predictive value for excluding significant fibrosis in primary care settings. A high DOC cut-off with 97.5% specificity could be used for detecting significant fibrosis (≥ F2) with an acceptable positive predictive value (87.1%). CONCLUSIONS This proof-of-concept study suggests that the DOC test may efficiently rule out and rule in significant liver fibrosis, thereby reducing the numbers of unnecessary liver biopsies. Moreover, the DOC test may be helpful for clinicians to exclude significant liver fibrosis in the general population.
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Affiliation(s)
- Lumin Yang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science, Anhui Agricultural University, No. 130 West Changjiang Lane, Hefei, Anhui, 230036, China
| | - Yafei Zhang
- Department of Infectious Diseases and Institute of Clinical Virology, The Second Hospital of Anhui Medical University, No. 678 Furong Lane, Hefei, Anhui, 230601, China
| | - Xiaodan Hong
- Department of Infectious Diseases and Institute of Clinical Virology, The Second Hospital of Anhui Medical University, No. 678 Furong Lane, Hefei, Anhui, 230601, China
| | - Ke Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science, Anhui Agricultural University, No. 130 West Changjiang Lane, Hefei, Anhui, 230036, China
| | - Bingyan Liu
- Department of Infectious Diseases and Institute of Clinical Virology, The Second Hospital of Anhui Medical University, No. 678 Furong Lane, Hefei, Anhui, 230601, China
| | - Peixin Zhang
- Department of Infectious Diseases and Institute of Clinical Virology, The Second Hospital of Anhui Medical University, No. 678 Furong Lane, Hefei, Anhui, 230601, China
| | - Qianqian Tang
- Department of Infectious Diseases and Institute of Clinical Virology, The Second Hospital of Anhui Medical University, No. 678 Furong Lane, Hefei, Anhui, 230601, China
| | - Jian Yu
- Department of Infectious Diseases and Institute of Clinical Virology, The Second Hospital of Anhui Medical University, No. 678 Furong Lane, Hefei, Anhui, 230601, China
| | - Xiao-Zhi Jin
- MAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Xin-Zhe Jin
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ni Zhang
- MAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Giovanni Targher
- Department of Medicine, University of Verona, Verona, Italy
- Metabolic Diseases Research Unit, IRCCS Sacro Cuore - Don Calabria Hospital, Negrar Di Valpolicella, Italy
| | - Christopher D Byrne
- Southampton National Institute for Health and Care Research Biomedical Research Centre, University Hospital Southampton and University of Southampton, Southampton General Hospital, Southampton, UK
| | - Zhenhua Zhang
- Department of Infectious Diseases and Institute of Clinical Virology, The Second Hospital of Anhui Medical University, No. 678 Furong Lane, Hefei, Anhui, 230601, China.
| | - Ming-Hua Zheng
- MAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China.
- Key Laboratory of Diagnosis and Treatment for the Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China.
| | - Jinsong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science, Anhui Agricultural University, No. 130 West Changjiang Lane, Hefei, Anhui, 230036, China.
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5
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Powell SM, Jarsberg LG, Zionce ELM, Anderson LN, Gritsenko MA, Nahid P, Jacobs JM. Longitudinal analysis of host protein serum signatures of treatment and recovery in pulmonary tuberculosis. PLoS One 2024; 19:e0294603. [PMID: 38421964 PMCID: PMC10903915 DOI: 10.1371/journal.pone.0294603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/03/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND A better understanding of treatment progression and recovery in pulmonary tuberculosis (TB) infectious disease is crucial. This study analyzed longitudinal serum samples from pulmonary TB patients undergoing interventional treatment to identify surrogate markers for TB-related outcomes. METHODS Serum that was collected at baseline and 8, 17, 26, and 52 weeks from 30 TB patients experiencing durable cure were evaluated and compared using a sensitive LC-MS/MS proteomic platform for the detection and quantification of differential host protein signatures relative to timepoint. The global proteome signature was analyzed for statistical differences across the time course and between disease severity and treatment groups. RESULTS A total of 676 proteins showed differential expression in the serum over these timepoints relative to baseline. Comparisons to understand serum protein dynamics at 8 weeks, treatment endpoints at 17 and 26 weeks, and post-treatment at 52 weeks were performed. The largest protein abundance changes were observed at 8 weeks as the initial effects of antibiotic treatment strongly impacted inflammatory and immune modulated responses. However, the largest number of proteome changes was observed at the end of treatment time points 17 and 26 weeks respectively. Post-treatment 52-week results showed an abatement of differential proteome signatures from end of treatment, though interestingly those proteins uniquely significant at post-treatment were almost exclusively downregulated. Patients were additionally stratified based upon disease severity and compared across all timepoints, identifying 461 discriminating proteome signatures. These proteome signatures collapsed into discrete expression profiles with distinct pathways across immune activation and signaling, hemostasis, and metabolism annotations. Insulin-like growth factor (IGF) and Integrin signaling maintained a severity signature through 52 weeks, implying an intrinsic disease severity signature well into the post-treatment timeframe. CONCLUSION Previous proteome studies have primarily focused on the 8-week timepoint in relation to culture conversion status. While this study confirms previous observations, it also highlights some differences. The inclusion of additional end of treatment and post-treatment time points offers a more comprehensive assessment of treatment progression within the serum proteome. Examining the expression dynamics at these later time periods will help in the investigation of relapse patients and has provided indicative markers of response and recovery.
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Affiliation(s)
- Samantha M. Powell
- Biologcal Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Leah G. Jarsberg
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Erin L. M. Zionce
- Earth Systems Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Lindsey N. Anderson
- Biologcal Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Marina A. Gritsenko
- Biologcal Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Jon M. Jacobs
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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6
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Zercher BP, Feng Y, Bush MF. Towards IM n with Electrostatic Drift Fields: Resetting the Potential of Trapped Ions Between Dimensions of Ion Mobility. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117163. [PMID: 37928050 PMCID: PMC10621600 DOI: 10.1016/j.ijms.2023.117163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Increasing the dimensionality of ion mobility (IM) presents an enticing opportunity to increase the information content and selectivity of many analyses. However, for implementations of IM that use constant electrostatic gradients to separate ions in a buffer gas, technical challenges have limited the adoption of the technique and number of dimensions within individual experiments. Here, we introduce a strategy to "reset" the potentials of ions between IM dimensions. To achieve this, mobility-selected ions are trapped between dimensions of IM, using a combination of RF and electrostatic fields, while the subsequent dimension of IM is devoid of any drift field. By applying an incremental voltage ramp, the potential of the trapping region is elevated, simultaneously establishing the drift field in the subsequent dimension of IM. The trapped ions are then released and separated. We measured similar arrival-time distributions of protein ions using this strategy and a method without potential resetting, suggesting that potential resetting can be performed without additional losses or activation of ions. The findings of those experiments were corroborated by ion trajectory simulations, which exhibited a very small changes in ion position and no significant changes in effective temperatures during potential resetting. Finally, we demonstrate that IM information can be preserved during potential resetting by selecting subpopulations of 9+ cytochrome c ions, resetting their potential, subjecting them to a second-dimension IM separation, and observing the retention of conformers within each subpopulation. We anticipate that this strategy will be useful for advancing flexible, multidimensional experiments on electrostatic IM instruments.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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7
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Argemi J, Kedia K, Gritsenko MA, Clemente-Sanchez A, Asghar A, Herranz JM, Liu ZX, Atkinson SR, Smith RD, Norden-Krichmar TM, Day LZ, Stolz A, Tayek JA, Bataller R, Morgan TR, Jacobs JM. Integrated Transcriptomic and Proteomic Analysis Identifies Plasma Biomarkers of Hepatocellular Failure in Alcohol-Associated Hepatitis. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1658-1669. [PMID: 36243044 PMCID: PMC9765311 DOI: 10.1016/j.ajpath.2022.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/08/2022] [Accepted: 08/31/2022] [Indexed: 11/07/2022]
Abstract
Alcohol-associated hepatitis (AH) is a form of liver failure with high short-term mortality. Recent studies have shown that defective function of hepatocyte nuclear factor 4 alpha (HNF4a) and systemic inflammation are major disease drivers of AH. Plasma biomarkers of hepatocyte function could be useful for diagnostic and prognostic purposes. Herein, an integrative analysis of hepatic RNA sequencing and liquid chromatography-tandem mass spectrometry was performed to identify plasma protein signatures for patients with mild and severe AH. Alcohol-related liver disease cirrhosis, nonalcoholic fatty liver disease, and healthy subjects were used as comparator groups. Levels of identified proteins primarily involved in hepatocellular function were decreased in patients with AH, which included hepatokines, clotting factors, complement cascade components, and hepatocyte growth activators. A protein signature of AH disease severity was identified, including thrombin, hepatocyte growth factor α, clusterin, human serum factor H-related protein, and kallistatin, which exhibited large abundance shifts between severe and nonsevere AH. The combination of thrombin and hepatocyte growth factor α discriminated between severe and nonsevere AH with high sensitivity and specificity. These findings were correlated with the liver expression of genes encoding secreted proteins in a similar cohort, finding a highly consistent plasma protein signature reflecting HNF4A and HNF1A functions. This unbiased proteomic-transcriptome analysis identified plasma protein signatures and pathways associated with disease severity, reflecting HNF4A/1A activity useful for diagnostic assessment in AH.
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Affiliation(s)
- Josepmaria Argemi
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania; Hepatology Program, Centro de Investigación Médica Aplicada, Liver Unit, Clinica Universidad de Navarra, Instituto de Investigacion de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Komal Kedia
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co, Inc., West Point, Pennsylvania
| | - Marina A Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Ana Clemente-Sanchez
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania; Biomedical Research Networking Center in Hepatic and Digestive Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Aliya Asghar
- Gasteroenterology Service, VA Long Beach Healthcare System, Long Beach, California
| | - Jose M Herranz
- Hepatology Program, Centro de Investigación Médica Aplicada, Liver Unit, Clinica Universidad de Navarra, Instituto de Investigacion de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Zhang-Xu Liu
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Stephen R Atkinson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Trina M Norden-Krichmar
- Department of Epidemiology, School of Medicine, University of California, Irvine, Irvine, California
| | - Le Z Day
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Andrew Stolz
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - John A Tayek
- Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Ramon Bataller
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Timothy R Morgan
- Gasteroenterology Service, VA Long Beach Healthcare System, Long Beach, California.
| | - Jon M Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington.
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Niu L, Thiele M, Geyer PE, Rasmussen DN, Webel HE, Santos A, Gupta R, Meier F, Strauss M, Kjaergaard M, Lindvig K, Jacobsen S, Rasmussen S, Hansen T, Krag A, Mann M. Noninvasive proteomic biomarkers for alcohol-related liver disease. Nat Med 2022; 28:1277-1287. [PMID: 35654907 PMCID: PMC9205783 DOI: 10.1038/s41591-022-01850-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/28/2022] [Indexed: 12/11/2022]
Abstract
Alcohol-related liver disease (ALD) is a major cause of liver-related death worldwide, yet understanding of the three key pathological features of the disease-fibrosis, inflammation and steatosis-remains incomplete. Here, we present a paired liver-plasma proteomics approach to infer molecular pathophysiology and to explore the diagnostic and prognostic capability of plasma proteomics in 596 individuals (137 controls and 459 individuals with ALD), 360 of whom had biopsy-based histological assessment. We analyzed all plasma samples and 79 liver biopsies using a mass spectrometry (MS)-based proteomics workflow with short gradient times and an enhanced, data-independent acquisition scheme in only 3 weeks of measurement time. In plasma and liver biopsy tissues, metabolic functions were downregulated whereas fibrosis-associated signaling and immune responses were upregulated. Machine learning models identified proteomics biomarker panels that detected significant fibrosis (receiver operating characteristic-area under the curve (ROC-AUC), 0.92, accuracy, 0.82) and mild inflammation (ROC-AUC, 0.87, accuracy, 0.79) more accurately than existing clinical assays (DeLong's test, P < 0.05). These biomarker panels were found to be accurate in prediction of future liver-related events and all-cause mortality, with a Harrell's C-index of 0.90 and 0.79, respectively. An independent validation cohort reproduced the diagnostic model performance, laying the foundation for routine MS-based liver disease testing.
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Affiliation(s)
- Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maja Thiele
- Odense Liver Research Centre, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- OmicEra Diagnostics, Planegg, Germany
| | - Ditlev Nytoft Rasmussen
- Odense Liver Research Centre, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Henry Emanuel Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rajat Gupta
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Pfizer Worldwide Research and Development, San Diego, CA, USA
| | - Florian Meier
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Functional Proteomics, Jena University Hospital, Jena, Germany
| | - Maximilian Strauss
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria Kjaergaard
- Odense Liver Research Centre, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Katrine Lindvig
- Odense Liver Research Centre, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Suganya Jacobsen
- Odense Liver Research Centre, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aleksander Krag
- Odense Liver Research Centre, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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10
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Bilbao A, Gibbons BC, Stow SM, Kyle JE, Bloodsworth KJ, Payne SH, Smith RD, Ibrahim YM, Baker ES, Fjeldsted JC. A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows. J Proteome Res 2022; 21:798-807. [PMID: 34382401 PMCID: PMC8837709 DOI: 10.1021/acs.jproteome.1c00425] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to improve the data quality of ion mobility-mass spectrometry (IM-MS) measurements is of great importance for enabling modular and efficient computational workflows and gaining better qualitative and quantitative insights from complex biological and environmental samples. We developed the PNNL PreProcessor, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format. Different experimental approaches are supported for IM-MS based on Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), including liquid chromatography (LC) and infusion analyses. The algorithms extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. Specifically, multidimensional smoothing improves peak shapes of poorly defined low-abundance signals, and saturation repair reconstructs the intensity profile of high-abundance peaks from various analyte types. Other functionalities are data compression and interpolation, IM demultiplexing, noise filtering by low intensity threshold and spike removal, and exporting of acquisition metadata. Several advantages of the tool are illustrated, including an increase of 19.4% in lipid annotations and a two-times faster processing of LC-DT IM-MS data-independent acquisition spectra from a complex lipid extract of a standard human plasma sample. The software is freely available at https://omics.pnl.gov/software/pnnl-preprocessor.
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Affiliation(s)
- Aivett Bilbao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bryson C Gibbons
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sarah M Stow
- Agilent Technologies, Santa Clara, California 95051, United States
| | - Jennifer E Kyle
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kent J Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - John C Fjeldsted
- Agilent Technologies, Santa Clara, California 95051, United States
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11
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da Silva KM, Iturrospe E, Heyrman J, Koelmel JP, Cuykx M, Vanhaecke T, Covaci A, van Nuijs ALN. Optimization of a liquid chromatography-ion mobility-high resolution mass spectrometry platform for untargeted lipidomics and application to HepaRG cell extracts. Talanta 2021; 235:122808. [PMID: 34517665 DOI: 10.1016/j.talanta.2021.122808] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/26/2022]
Abstract
Analytical methods to evaluate the lipidome of biological samples need to provide high data quality to ensure comprehensive profiling and reliable structural elucidation. In this perspective, liquid chromatography-high resolution mass spectrometry (LC-HRMS) is the state-of-the-art technique for lipidomic analysis of biological samples. There are thousands of lipids in most biological samples, and therefore separation methods before introduction to the mass spectrometer is key for relative quantitation and identification. Chromatographic methods differ across laboratories, without any consensus on the best methodologies. Therefore, we designed an experiment to determine the optimal LC methodology, and assessed the value of ion mobility for an additional dimension of separation. To apply an untargeted method for hypothesis generation focused on lipidomics, LC-HRMS parameters were optimized based on the measurement of 50 panel lipids covering key human metabolic pathways. Reversed-phase liquid chromatography columns were compared based on a quality scoring system considering the signal-to-noise ratio, peak shape, and retention factor. Furthermore, drift tube ion mobility spectrometry (DTIMS) was implemented to increase peak capacity and confidence during annotation by providing collision cross section (CCS) values for the analytes under investigation. However, hyphenating DTIMS to LC-HRMS may result in a reduced sensitivity due to impaired duty cycles. To increase the signal intensity, a Box-Behnken design (BBD) was used to optimize four key factors, i.e. drift entrance voltage, drift exit voltage, rear funnel entrance, and rear funnel exit voltages. Application of a maximized desirability function provided voltages for the above-mentioned parameters resulting in higher signal intensity compared to each combination of parameters used during the BBD. In addition, the influence of single pulse and Hadamard 4-bit multiplexed modes on signal intensity was explored and different trap filling and release times of ions were evaluated. The optimized LC-DTIM-HRMS platform was applied to extracts from HepaRG cells and resulted in 3912 high-quality features (<30% median relative standard deviation; n = 6, t = 24 h). From these features, 436 lipid species could be annotated (i.e., matching based on accurate mass <5 ppm, isotopic pattern, in-silico MS/MS fragmentation, and in-silico CCS database matching <3%). The application of LC-DTIM-HRMS for untargeted analysis workflows is growing and the platform optimization, as described here, can be used to guide the method development and CCS database comparison for high confidence lipid annotation.
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Affiliation(s)
| | - Elias Iturrospe
- University of Antwerp, Toxicological Centre, Universiteitsplein 1, 2610, Antwerp, Belgium; Vrije Universiteit Brussel, Department of In Vitro Toxicology and Dermato-cosmetology, Laarbeeklaan 103, 1090, Jette, Belgium
| | - Joris Heyrman
- University of Antwerp, Toxicological Centre, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Jeremy P Koelmel
- Yale University, School of Public Health, New Haven, CT, 06520, United States
| | - Matthias Cuykx
- Antwerp University Hospital, Laboratory of Clinical Medicine, Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - Tamara Vanhaecke
- Vrije Universiteit Brussel, Department of In Vitro Toxicology and Dermato-cosmetology, Laarbeeklaan 103, 1090, Jette, Belgium
| | - Adrian Covaci
- University of Antwerp, Toxicological Centre, Universiteitsplein 1, 2610, Antwerp, Belgium
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12
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Jarsberg LG, Kedia K, Wendler J, Wright AT, Piehowski PD, Gritsenko MA, Shi T, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Keane J, Jacobs JM, Nahid P. Nutritional markers and proteome in patients undergoing treatment for pulmonary tuberculosis differ by geographic region. PLoS One 2021; 16:e0250586. [PMID: 33951066 PMCID: PMC8099102 DOI: 10.1371/journal.pone.0250586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/09/2021] [Indexed: 11/24/2022] Open
Abstract
Introduction Contemporary phase 2 TB disease treatment clinical trials have found that microbiologic treatment responses differ between African versus non-African regions, the reasons for which remain unclear. Understanding host and disease phenotypes that may vary by region is important for optimizing curative treatments. Methods We characterized clinical features and the serum proteome of phase 2 TB clinical trial participants undergoing treatment for smear positive, culture-confirmed TB, comparing host serum protein expression in clinical trial participants enrolled in African and Non-African regions. Serum samples were collected from 289 participants enrolled in the Centers for Disease Control and Prevention TBTC Study 29 (NCT00694629) at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Results After a peptide level proteome analysis utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS) and subsequent statistical analysis, a total of 183 core proteins demonstrated significant differences at both baseline and at week 8 timepoints between participants enrolled from African and non-African regions. The majority of the differentially expressed proteins were upregulated in participants from the African region, and included acute phase proteins, mediators of inflammation, as well as coagulation and complement pathways. Downregulated proteins in the African population were primarily linked to nutritional status and lipid metabolism pathways. Conclusions We have identified differentially expressed nutrition and lipid pathway proteins by geographic region in TB patients undergoing treatment for pulmonary tuberculosis, which appear to be associated with differential treatment responses. Future TB clinical trials should collect expanded measures of nutritional status and further evaluate the relationship between nutrition and microbiologic treatment response.
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Affiliation(s)
- Leah G. Jarsberg
- Division of Pulmonary and Critical Care Medicine and UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, California, United States of America
| | - Komal Kedia
- Department of Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM) Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | - Jason Wendler
- Seattle Children’s Hospital, Seattle, Washington, United States of America
| | - Aaron T. Wright
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Paul D. Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Marina A. Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David M. Lewinsohn
- Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, Oregon, United States of America
| | - George B. Sigal
- Meso Scale Diagnostics, Rockville, Maryland, United States of America
| | - Marc H. Weiner
- University of Texas Health Science Center at San Antonio and the South Texas VAMC, San Antonio, Texas, United States of America
| | - Richard D. Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Joseph Keane
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, Dublin, Ireland
| | - Jon M. Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine and UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, California, United States of America
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13
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Brown CJ, Gaunitz S, Wang Z, Strindelius L, Jacobson SC, Clemmer DE, Trinidad JC, Novotny MV. Glycoproteomic Analysis of Human Urinary Exosomes. Anal Chem 2020; 92:14357-14365. [PMID: 32985870 PMCID: PMC7875506 DOI: 10.1021/acs.analchem.0c01952] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Exosomes represent a class of secreted biological vesicles, which have recently gained attention due to their function as intertissue and interorganism transporters of genetic materials, small molecules, lipids, and proteins. Although the protein constituents of these exosomes are often glycosylated, a large-scale characterization of the glycoproteome has not yet been completed. This study identified 3144 unique glycosylation events belonging to 378 glycoproteins and 604 unique protein sites of glycosylation. With these data, we investigated the level of glycan microheterogeneity within the urinary exosomes, finding on average 5.9 glycans per site. The glycan family abundance on individual proteins showed subtle differences, providing an additional level of molecular characterization compared to the unmodified proteome. Finally, we show protein site-specific changes in regard to the common urinary glycoprotein, uromodulin. While uromodulin is an individual case, these same site-specific analyses provide a way forward for developing diagnostic glycoprotein biomarkers with urine as a noninvasive biological fluid. This study represents an important first step in understanding the functional urinary glycoproteome.
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Affiliation(s)
- Christopher J Brown
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Stefan Gaunitz
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Ziyu Wang
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Lena Strindelius
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Stephen C Jacobson
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Milos V Novotny
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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14
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Orwoll ES, Wiedrick J, Nielson CM, Jacobs J, Baker ES, Piehowski P, Petyuk V, Gao Y, Shi T, Smith RD, Bauer DC, Cummings SR, Lapidus J. Proteomic assessment of serum biomarkers of longevity in older men. Aging Cell 2020; 19:e13253. [PMID: 33078901 PMCID: PMC7681066 DOI: 10.1111/acel.13253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/30/2020] [Accepted: 08/30/2020] [Indexed: 12/28/2022] Open
Abstract
The biological bases of longevity are not well understood, and there are limited biomarkers for the prediction of long life. We used a high-throughput, discovery-based proteomics approach to identify serum peptides and proteins that were associated with the attainment of longevity in a longitudinal study of community-dwelling men age ≥65 years. Baseline serum in 1196 men were analyzed using liquid chromatography-ion mobility-mass spectrometry, and lifespan was determined during ~12 years of follow-up. Men who achieved longevity (≥90% expected survival) were compared to those who died earlier. Rigorous statistical methods that controlled for false positivity were utilized to identify 25 proteins that were associated with longevity. All these proteins were in lower abundance in long-lived men and included a variety involved in inflammation or complement activation. Lower levels of longevity-associated proteins were also associated with better health status, but as time to death shortened, levels of these proteins increased. Pathway analyses implicated a number of compounds as important upstream regulators of the proteins and implicated shared networks that underlie the observed associations with longevity. Overall, these results suggest that complex pathways, prominently including inflammation, are linked to the likelihood of attaining longevity. This work may serve to identify novel biomarkers for longevity and to understand the biology underlying lifespan.
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Affiliation(s)
| | | | | | - Jon Jacobs
- Biological Science Division Pacific Northwest National Laboratory Richland WA USA
| | - Erin S. Baker
- Department of Chemistry North Carolina State University Raleigh NC USA
| | - Paul Piehowski
- Biological Science Division Pacific Northwest National Laboratory Richland WA USA
| | - Vladislav Petyuk
- Biological Science Division Pacific Northwest National Laboratory Richland WA USA
| | - Yuqian Gao
- Biological Science Division Pacific Northwest National Laboratory Richland WA USA
| | - Tujin Shi
- Biological Science Division Pacific Northwest National Laboratory Richland WA USA
| | - Richard D. Smith
- Biological Science Division Pacific Northwest National Laboratory Richland WA USA
| | - Douglas C. Bauer
- Departments of Medicine and Epidemiology & Biostatistics University of California San Francisco CA USA
| | - Steven R. Cummings
- California Pacific Medical Center Research Institute San Francisco CA USA
| | - Jodi Lapidus
- Oregon Health & Science University Portland OR USA
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15
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Alcazar O, Hernandez LF, Nakayasu ES, Piehowski PD, Ansong C, Abdulreda MH, Buchwald P. Longitudinal proteomics analysis in the immediate microenvironment of islet allografts during progression of rejection. J Proteomics 2020; 223:103826. [PMID: 32442648 DOI: 10.1016/j.jprot.2020.103826] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The applicability and benefits of pancreatic islet transplantation are limited due to various issues including the need to avoid immune-mediated rejection. Here, we used our experimental platform of allogeneic islet transplant in the anterior chamber of the eye (ACE-platform) to longitudinally monitor the progress of rejection in mice and obtain aqueous humor samples representative of the microenvironment of the graft for accurately-timed proteomic analyses. LC-MS/MS-based proteomics performed on such mass-limited samples (~5 μL) identified a total of 1296 proteins. Various analyses revealed distinct protein patterns associated with the mounting of the inflammatory and immune responses and their evolution with the progression of the rejection. Pathway analyses indicated predominant changes in cytotoxic functions, cell movement, and innate and adaptive immune responses. Network prediction analyses revealed transition from humoral to cellular immune response and exacerbation of pro-inflammatory signaling. One of the proteins identified by this localized proteomics as a candidate biomarker of islet rejection, Cystatin 3, was further validated by ELISA in the aqueous humor. This study provides (1) experimental evidence demonstrating the feasibility of longitudinal localized proteomics using small aqueous humor samples and (2) proof-of-concept for the discovery of biomarkers of impending immune attack from the immediate local microenvironment of ACE-transplanted islets. SIGNIFICANCE: The combination of the ACE-platform and longitudinal localized proteomics offers a powerful approach to biomarker discovery during the various stages of immune reactions mounted against transplanted tissues including pancreatic islets. It also supports proteomics-assisted drug discovery and development efforts aimed at preventing rejection through efficacy assessment of new agents by noninvasive and longitudinal graft monitoring.
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Affiliation(s)
- Oscar Alcazar
- University of Miami Miller School of Medicine, Diabetes Research Institute, Miami, FL, USA
| | - Luis F Hernandez
- University of Miami Miller School of Medicine, Diabetes Research Institute, Miami, FL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Midhat H Abdulreda
- University of Miami Miller School of Medicine, Diabetes Research Institute, Miami, FL, USA; University of Miami Miller School of Medicine, Department of Surgery, Miami, FL, USA; University of Miami Miller School of Medicine, Department of Microbiology and Immunology, Miami, FL, USA; University of Miami Miller School of Medicine, Department of Ophthalmology, Miami, FL, USA.
| | - Peter Buchwald
- University of Miami Miller School of Medicine, Diabetes Research Institute, Miami, FL, USA; University of Miami Miller School of Medicine, Department of Molecular and Cellular Pharmacology, Miami, FL, USA.
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16
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Morris CB, Poland JC, May JC, McLean JA. Fundamentals of Ion Mobility-Mass Spectrometry for the Analysis of Biomolecules. Methods Mol Biol 2020; 2084:1-31. [PMID: 31729651 DOI: 10.1007/978-1-0716-0030-6_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for both the instrumental arrangements and key application areas that are commonly encountered in bioanalytical settings. New advances in these high-throughput strategies are described with description of complementary informatics tools to effectively utilize these data-intensive measurements. Rapid separations such as these are especially important in systems, synthetic, and chemical biology in which many small molecules are transient and correspond to various biological classes for integrated omics measurements. This chapter highlights the fundamentals of IM-MS and its applications toward biomolecular separations and discusses methods currently being used in the fields of proteomics, lipidomics, and metabolomics.
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Affiliation(s)
- Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - James C Poland
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - Jody C May
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA. .,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA.
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17
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McKenna KR, Li L, Krishnamurthy R, Liotta CL, Fernández FM. Organic acid shift reagents for the discrimination of carbohydrate isobars by ion mobility-mass spectrometry. Analyst 2020; 145:8008-8015. [DOI: 10.1039/d0an01546f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Traveling wave and drift tube ion mobility were utilized to separate isomeric disaccharides. Organic acid shift reagents were necessary to increase the resolution of these separations for mixture analysis.
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Affiliation(s)
- Kristin R. McKenna
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
| | - Li Li
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
| | | | - Charles L. Liotta
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
| | - Facundo M. Fernández
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
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18
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Fundamentals and applications of incorporating chromatographic separations with ion mobility-mass spectrometry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115625] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Reinecke T, Naylor CN, Clowers BH. Ion multiplexing: Maximizing throughput and signal to noise ratio for ion mobility spectrometry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES. Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples. Trends Analyt Chem 2019; 116:292-299. [PMID: 31798197 DOI: 10.1016/j.trac.2019.04.022] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.
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Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A &M University, College Station, TX
| | - James N Dodds
- Department of Chemistry, NC State University, Raleigh, NC
| | - Jeremy Ash
- Department of Chemistry, NC State University, Raleigh, NC
| | - Denis Fourches
- Department of Chemistry, NC State University, Raleigh, NC
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Jason P Wendler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Erin S Baker
- Department of Chemistry, NC State University, Raleigh, NC
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21
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Romero KI, Fernandez-Maestre R. Ion mobility spectrometry: the diagnostic tool of third millennium medicine. Rev Assoc Med Bras (1992) 2019; 64:861-868. [PMID: 30673009 DOI: 10.1590/1806-9282.64.09.861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 01/13/2018] [Indexed: 11/22/2022] Open
Abstract
Ion mobility spectrometry (IMS) is a fast, low cost, portable, and sensitive technique that separates ions in a drift tube under the influence of an electric field according to their size and shape. IMS represents a non-invasive and reliable instrumental alternative for the diagnosis of different diseases through the analysis of volatile metabolites in biological samples. IMS has applications in medicine in the study of volatile compounds for the non-invasive diagnose of bronchial carcinoma, chronic obstructive pulmonary disease, and other diseases analysing breath, urine, blood, faeces, and other biological samples. This technique has been used to study complex mixtures such as proteomes, metabolomes, complete organisms like bacteria and viruses, monitor anaesthetic agents, determine drugs, pharmaceuticals, and volatile compounds in human body fluids, and others. Pharmaceutical applications include analysis of over-the-counter-drugs, quality assessment, and cleaning verification. Medical practice needs non-invasive, robust, secure, fast, real-time, and low-cost methods with high sensitivity and compact size instruments to diagnose different diseases and IMS is the diagnostic tool that meets all these requirements of the Medicine of the future.
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Affiliation(s)
- Katiuska I Romero
- . Medical Subdirector, Organización Clínica Bonnadona Prevenir, Barranquilla, Atlantico, Colombia
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Chouinard CD, Nagy G, Webb IK, Shi T, Baker ES, Prost SA, Liu T, Ibrahim YM, Smith RD. Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry. Anal Chem 2018; 90:10889-10896. [PMID: 30118596 PMCID: PMC6211290 DOI: 10.1021/acs.analchem.8b02397] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphoproteomics greatly augments proteomics and holds tremendous potential for insights into the modulation of biological systems for various disease states. However, numerous challenges hinder conventional methods in terms of measurement sensitivity, throughput, quantification, and capabilities for confident phosphopeptide and phosphosite identification. In this work, we report the first example of integrating structures for lossless ion manipulations ion mobility-mass spectrometry (SLIM IM-MS) with online reversed-phase liquid chromatography (LC) to evaluate its potential for addressing the aforementioned challenges. A mixture of 51 heavy-labeled phosphopeptides was analyzed with a SLIM IM module having integrated ion accumulation and long-path separation regions. The SLIM IM-MS provided limits of detection as low as 50-100 pM (50-100 amol/μL) for several phosphopeptides, with the potential for significant further improvements. In addition, conventionally problematic phosphopeptide isomers could be resolved following an 18 m SLIM IM separation. The 2-D LC-IM peak capacity was estimated as ∼9000 for a 90 min LC separation coupled to an 18 m SLIM IM separation, considerably higher than LC alone and providing a basis for both improved identification and quantification, with additional gains projected with the future use of longer path SLIM IM separations. Thus, LC-SLIM IM-MS offers great potential for improving the sensitivity, separation, and throughput of phosphoproteomics analyses.
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Affiliation(s)
- Christopher D. Chouinard
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ian K. Webb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin S. Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Spencer A. Prost
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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24
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Otwell AE, Callister SJ, Sherwood RW, Zhang S, Goldman AR, Smith RD, Richardson RE. Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA. GEOBIOLOGY 2018; 16:522-539. [PMID: 29905980 DOI: 10.1111/gbi.12295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
We established Fe(III)-reducing co-cultures of two species of metal-reducing bacteria, the Gram-positive Desulfotomaculum reducens MI-1 and the Gram-negative Geobacter sulfurreducens PCA. Co-cultures were given pyruvate, a substrate that D. reducens can ferment and use as electron donor for Fe(III) reduction. G. sulfurreducens relied upon products of pyruvate oxidation by D. reducens (acetate, hydrogen) for use as electron donor in the co-culture. Co-cultures reduced Fe(III) to Fe(II) robustly, and Fe(II) was consistently detected earlier in co-cultures than pure cultures. Notably, faster cell growth, and correspondingly faster pyruvate oxidation, was observed by D. reducens in co-cultures. Global comparative proteomic analysis was performed to observe differential protein abundance during co-culture vs. pure culture growth. Proteins previously associated with Fe(III) reduction in G. sulfurreducens, namely c-type cytochromes and type IV pili proteins, were significantly increased in abundance in co-cultures relative to pure cultures. D. reducens ribosomal proteins were significantly increased in co-cultures, likely a reflection of faster growth rates observed for D. reducens cells while in co-culture. Furthermore, we developed multiple reaction monitoring (MRM) assays to quantitate specific biomarker peptides. The assays were validated in pure and co-cultures, and protein abundance ratios from targeted MRM and global proteomic analysis correlate significantly.
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Affiliation(s)
- Anne E Otwell
- Department of Microbiology, Cornell University, Ithaca, New York
| | | | - Robert W Sherwood
- Proteomics and Mass Spectrometry Facility, Cornell University, Ithaca, New York
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Facility, Cornell University, Ithaca, New York
| | - Abby R Goldman
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York
| | | | - Ruth E Richardson
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, New York
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25
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Kedia K, Wendler JP, Baker ES, Burnum-Johnson KE, Jarsberg LG, Stratton KG, Wright AT, Piehowski PD, Gritsenko MA, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Jacobs JM, Nahid P. Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis. Tuberculosis (Edinb) 2018; 112:52-61. [PMID: 30205969 PMCID: PMC6181582 DOI: 10.1016/j.tube.2018.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/22/2023]
Abstract
Rationale: The monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment. Objective: We utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy. Methods: Serum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points. Results: A total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status. Conclusion: A comprehensive host serum protein dataset reflective of TB treatment effect is defined. A repeating set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2, among others) were found to change significantly in response to treatment, to strongly correlate with culture status, and at baseline to be predictive of future culture conversion. If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care.
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Affiliation(s)
- Komal Kedia
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason P Wendler
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erin S Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Leah G Jarsberg
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kelly G Stratton
- Computational and Statistical Analysis Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aaron T Wright
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Lewinsohn
- Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
| | | | - Marc H Weiner
- University of Texas Health Science Center at San Antonio and the South Texas VAMC, San Antonio, TX, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jon M Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
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26
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A chemometric approach for characterization of serum transthyretin in familial amyloidotic polyneuropathy type I (FAP-I) by electrospray ionization-ion mobility mass spectrometry. Talanta 2018; 181:87-94. [DOI: 10.1016/j.talanta.2017.12.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 01/19/2023]
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27
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Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry. Bioanalysis 2018; 10:279-289. [PMID: 29494212 DOI: 10.4155/bio-2017-0245] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AIM Lipid mediators (LMs) are broadly defined as a class of bioactive lipophilic molecules that regulate cell-to-cell communication events with many having a strong correlation with various human diseases and conditions. LMs are usually analyzed with LC-MS, but their numerous isomers greatly complicate the measurements with essentially identical fragmentation spectra and LC separations are not always sufficient for distinguishing the features. Results/methodology: In this work, we characterized LMs using ion mobility spectrometry (IMS) coupled with MS (IMS-MS). The collision cross-sections and m/z values from the IMS and MS analyses displayed distinct trend lines. Specifically, the structural trend lines for sodiated LMs originating from docosahexaenoic acid had the smallest collision cross-section values in relation to m/z, while those from linoleic acid had the largest. LC-IMS-MS analyses were also performed on LMs in flu infected mouse tissue samples. These multidimensional studies were able to assess known LMs while also detecting new species. CONCLUSION Adding IMS separations to conventional LC-MS analyses show great utility for enabling better identification and characterization of LMs in complex biological samples.
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Ion mobility in the pharmaceutical industry: an established biophysical technique or still niche? Curr Opin Chem Biol 2018; 42:147-159. [DOI: 10.1016/j.cbpa.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/10/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]
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29
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Nielson CM, Wiedrick J, Shen J, Jacobs J, Baker ES, Baraff A, Piehowski P, Lee CG, Baratt A, Petyuk V, McWeeney S, Lim JY, Bauer DC, Lane NE, Cawthon PM, Smith RD, Lapidus J, Orwoll ES. Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics. J Bone Miner Res 2017; 32:1559-1567. [PMID: 28316103 PMCID: PMC5489383 DOI: 10.1002/jbmr.3125] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/22/2017] [Accepted: 03/06/2017] [Indexed: 01/16/2023]
Abstract
Serum proteomics analysis may lead to the discovery of novel osteoporosis biomarkers. The Osteoporotic Fractures in Men (MrOS) study comprises men ≥65 years old in the US who have had repeated BMD measures and have been followed for incident fracture. High-throughput quantitative proteomic analysis was performed on baseline fasting serum samples from non-Hispanic white men using a multidimensional approach coupling liquid chromatography, ion-mobility separation, and mass spectrometry (LC-IMS-MS). We followed the participants for a mean of 4.6 years for changes in femoral neck bone mineral density (BMD) and for incident hip fracture. Change in BMD was determined from mixed effects regression models taking age and weight into account. Participants were categorized into three groups: BMD maintenance (no decline; estimated change ≥0 g/cm2 , n = 453); expected loss (estimated change 0 to 1 SD below the estimated mean change, -0.034 g/cm2 for femoral neck, n = 1184); and accelerated loss (estimated change ≥1 SD below mean change, n = 237). Differential abundance values of 3946 peptides were summarized by meta-analysis to determine differential abundance of each of 339 corresponding proteins for accelerated BMD loss versus maintenance. Using this meta-analytic standardized fold change at cutoffs of ≥1.1 or ≤0.9 (p < 0.10), 20 proteins were associated with accelerated BMD loss. Associations of those 20 proteins with incident hip fracture were tested using Cox proportional hazards models with age and BMI adjustment in 2473 men. Five proteins were associated with incident hip fracture (HR between 1.29 and 1.41 per SD increase in estimated protein abundance). Some proteins have been previously associated with fracture risk (eg, CD14 and SHBG), whereas others have roles in cellular senescence and aging (B2MG and TIMP1) and complement activation and innate immunity (CO7, CO9, CFAD). These findings may inform development of biomarkers for future research in bone biology and fracture prediction. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Carrie M Nielson
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
- Bone and Mineral Unit, Oregon Health & Science University, Portland, OR, USA
| | - Jack Wiedrick
- Biostatistics and Design Program, OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Jian Shen
- Bone and Mineral Unit, Oregon Health & Science University, Portland, OR, USA
| | - Jon Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aaron Baraff
- Division of Biostatistics, Oregon Health & Science University, Portland, OR, USA
| | - Paul Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Christine G Lee
- Research Service, Portland Veterans Affairs Medical Center, Portland, OR, USA
| | - Arie Baratt
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA
| | - Vladislav Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA
| | - Jeong Youn Lim
- Division of Biostatistics, Oregon Health & Science University, Portland, OR, USA
| | - Douglas C Bauer
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Nancy E Lane
- Department of Internal Medicine, University of California at Davis, Sacramento, CA, USA
| | - Peggy M Cawthon
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jodi Lapidus
- Biostatistics and Design Program, OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Eric S Orwoll
- Bone and Mineral Unit, Oregon Health & Science University, Portland, OR, USA
- Department of Medicine, Oregon Health & Science University, Portland, OR, USA
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30
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Zheng X, Wojcik R, Zhang X, Ibrahim YM, Burnum-Johnson KE, Orton DJ, Monroe ME, Moore RJ, Smith RD, Baker ES. Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:71-92. [PMID: 28301728 PMCID: PMC5627998 DOI: 10.1146/annurev-anchem-061516-045212] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits.
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Affiliation(s)
- Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Roza Wojcik
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Xing Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Anschutz Medical Campus, University of Colorado, Denver, Colorado 80045
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Daniel J Orton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Matthew E Monroe
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Ronald J Moore
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Erin S Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
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Wang Z, Wang C, Liu S, He W, Wang L, Gan J, Huang Z, Wang Z, Wei H, Zhang J, Dong L. Specifically Formed Corona on Silica Nanoparticles Enhances Transforming Growth Factor β1 Activity in Triggering Lung Fibrosis. ACS NANO 2017; 11:1659-1672. [PMID: 28085241 DOI: 10.1021/acsnano.6b07461] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A corona is a layer of macromolecules formed on a nanoparticle surface in vivo. It can substantially change the biological identity of nanomaterials and possibly trigger adverse responses from the body tissues. Dissecting the role of the corona in the development of a particular disease may provide profound insights for understanding toxicity of nanomaterials in general. In our present study, we explored the capability of different silica nanoparticles (SiNPs) to induce silicosis in the mouse lung and analyzed the composition of coronas formed on these particles. We found that SiNPs of certain size and surface chemistry could specifically recruit transforming growth factor β1 (TGF-β1) into their corona, which subsequently induces the development of lung fibrosis. Once embedded into the corona on SiNPs, TGF-β1 was remarkably more stable than in its free form, and its fibrosis-triggering activity was significantly prolonged. Our study meaningfully demonstrates that a specific corona component on a certain nanoparticle could initiate a particular pathogenic process in a clinically relevant disease model. Our findings may shed light on the understanding of molecular mechanisms of human health risks correlated with exposure to small-scale substances.
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Affiliation(s)
- Zhenzhen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Taipa, Macau SAR, China
| | - Shang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - Wei He
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - Lintao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - JingJing Gan
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - Zhen Huang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - Zhenheng Wang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - Haoyang Wei
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
- Jiangsu Provincial Laboratory for Nano-Technology, Nanjing University , Nanjing 210093, China
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University , 163 Xianlin Avenue, Nanjing 210093, China
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32
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Khadempour L, Burnum-Johnson KE, Baker ES, Nicora CD, Webb-Robertson BJM, White RA, Monroe ME, Huang EL, Smith RD, Currie CR. The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates. Mol Ecol 2016; 25:5795-5805. [PMID: 27696597 DOI: 10.1111/mec.13872] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/17/2016] [Accepted: 09/19/2016] [Indexed: 01/20/2023]
Abstract
Herbivores use symbiotic microbes to help derive energy and nutrients from plant material. Leaf-cutter ants are a paradigmatic example, cultivating their mutualistic fungus Leucoagaricus gongylophorus on plant biomass that workers forage from a diverse collection of plant species. Here, we investigate the metabolic flexibility of the ants' fungal cultivar for utilizing different plant biomass. Using feeding experiments and a novel approach in metaproteomics, we examine the enzymatic response of L. gongylophorus to leaves, flowers, oats or a mixture of all three. Across all treatments, our analysis identified and quantified 1766 different fungal proteins, including 161 putative biomass-degrading enzymes. We found significant differences in the protein profiles in the fungus gardens of subcolonies fed different plant substrates. When provided with leaves or flowers, which contain the majority of their energy as recalcitrant plant polymers, the fungus gardens produced more proteins predicted to break down cellulose: endoglucanase, exoglucanase and β-glucosidase. Further, the complete metaproteomes for the leaves and flowers treatments were very similar, while the mixed substrate treatment closely resembled the treatment with oats alone. This indicates that when provided a mixture of plant substrates, fungus gardens preferentially break down the simpler, more digestible substrates. This flexible, substrate-specific enzymatic response of the fungal cultivar allows leaf-cutter ants to derive energy from a wide range of substrates, which likely contributes to their ability to be dominant generalist herbivores.
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Affiliation(s)
- Lily Khadempour
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Zoology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Richard A White
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Eric L Huang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
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34
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Burnum-Johnson KE, Nie S, Casey CP, Monroe ME, Orton DJ, Ibrahim YM, Gritsenko MA, Clauss TRW, Shukla AK, Moore RJ, Purvine SO, Shi T, Qian W, Liu T, Baker ES, Smith RD. Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry. Mol Cell Proteomics 2016; 15:3694-3705. [PMID: 27670688 DOI: 10.1074/mcp.m116.061143] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/23/2016] [Indexed: 12/16/2022] Open
Abstract
Current proteomic approaches include both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g. candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches, however, suffer from limitations. Discovery measurements aim to sample the whole proteome but have lower sensitivity, accuracy, and quantitation precision than targeted approaches, whereas targeted measurements are significantly more sensitive but only sample a limited portion of the proteome. Herein, we describe a new approach that performs both discovery and targeted monitoring (DTM) in a single analysis by combining liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled target peptides are spiked into tryptic digests and both the labeled and unlabeled peptides are detected using LC-IMS-MS instrumentation. Compared with the broad LC-MS discovery measurements, DTM yields greater peptide/protein coverage and detects lower abundance species. DTM also achieved detection limits similar to selected reaction monitoring (SRM) indicating its potential for combined high quality discovery and targeted analyses, which is a significant step toward the convergence of discovery and targeted approaches.
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Affiliation(s)
- Kristin E Burnum-Johnson
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Song Nie
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Cameron P Casey
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Matthew E Monroe
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Daniel J Orton
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Yehia M Ibrahim
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Marina A Gritsenko
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Therese R W Clauss
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Anil K Shukla
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Ronald J Moore
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Samuel O Purvine
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Tujin Shi
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Weijun Qian
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Tao Liu
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Erin S Baker
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Richard D Smith
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
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35
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Deng L, Ibrahim YM, Baker ES, Aly NA, Hamid AM, Zhang X, Zheng X, Garimella SVB, Webb IK, Prost SA, Sandoval JA, Norheim RV, Anderson GA, Tolmachev AV, Smith RD. Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry. ChemistrySelect 2016; 1:2396-2399. [PMID: 28936476 DOI: 10.1002/slct.201600460] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mass spectrometry (MS)-based multi-omic measurements, including proteomics, metabolomics, lipidomics, and glycomics, are increasingly transforming our ability to characterize and understand biological systems. Multi-omic analyses and the desire for comprehensive measurement coverage presently have limitations due to the chemical diversity and range of abundances of biomolecules in complex samples. Advances addressing these challenges increasingly are based upon the ability to quickly separate, react and otherwise manipulate sample components for analysis by MS. Here we report on a new approach using Structures for Lossless Ion Manipulations (SLIM) to enable long serpentine path ion mobility spectrometry (IMS) separations followed by MS analyses. This approach provides previously unachieved resolution for biomolecular species, in conjunction with more effective ion utilization, and a basis for greatly improved characterization of very small sample sizes.
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Affiliation(s)
- Liulin Deng
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Yehia M Ibrahim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Erin S Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Noor A Aly
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Ahmed M Hamid
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Xing Zhang
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Xueyun Zheng
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Sandilya V B Garimella
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Ian K Webb
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Spencer A Prost
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Jeremy A Sandoval
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Randolph V Norheim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Gordon A Anderson
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Aleksey V Tolmachev
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
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36
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May JC, Gant-Branum RL, McLean JA. Targeting the untargeted in molecular phenomics with structurally-selective ion mobility-mass spectrometry. Curr Opin Biotechnol 2016; 39:192-197. [PMID: 27132126 DOI: 10.1016/j.copbio.2016.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/06/2016] [Accepted: 04/13/2016] [Indexed: 12/25/2022]
Abstract
Systems-wide molecular phenomics is rapidly expanding through technological advances in instrumentation and bioinformatics. Strategies such as structural mass spectrometry, which utilizes size and shape measurements with molecular weight, serve to characterize the sum of molecular expression in biological contexts, where broad-scale measurements are made that are interpreted through big data statistical techniques to reveal underlying patterns corresponding to phenotype. The data density, data dimensionality, data projection, and data interrogation are all critical aspects of these approaches to turn data into salient information. Untargeted molecular phenomics is already having a dramatic impact in discovery science from drug discovery to synthetic biology. It is evident that these emerging techniques will integrate closely in broad efforts aimed at precision medicine.
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Affiliation(s)
- Jody Christopher May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Randi Lee Gant-Branum
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - John Allen McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA.
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38
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Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient. Proc Natl Acad Sci U S A 2016; 113:1381-6. [PMID: 26787912 DOI: 10.1073/pnas.1523434113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Compensatory signaling pathways in tumors confer resistance to targeted therapy, but the pathways and their mechanisms of activation remain largely unknown. We describe a procedure for quantitative proteomics and phosphoproteomics on snap-frozen biopsies of hepatocellular carcinoma (HCC) and matched nontumor liver tissue. We applied this procedure to monitor signaling pathways in serial biopsies taken from an HCC patient before and during treatment with the multikinase inhibitor sorafenib. At diagnosis, the patient had an advanced HCC. At the time of the second biopsy, abdominal imaging revealed progressive disease despite sorafenib treatment. Sorafenib was confirmed to inhibit MAPK signaling in the tumor, as measured by reduced ribosomal protein S6 kinase phosphorylation. Hierarchical clustering and enrichment analysis revealed pathways broadly implicated in tumor progression and resistance, such as epithelial-to-mesenchymal transition and cell adhesion pathways. Thus, we describe a protocol for quantitative analysis of oncogenic pathways in HCC biopsies and obtained first insights into the effect of sorafenib in vivo. This protocol will allow elucidation of mechanisms of resistance and enable precision medicine.
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39
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Szymańska E, Davies AN, Buydens LMC. Chemometrics for ion mobility spectrometry data: recent advances and future prospects. Analyst 2016; 141:5689-5708. [DOI: 10.1039/c6an01008c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This is the first comprehensive review on chemometric techniques used in ion mobility spectrometry data analysis.
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Affiliation(s)
- Ewa Szymańska
- Radboud University
- Institute for Molecules and Materials
- 6500 GL Nijmegen
- The Netherlands
- TI-COAST
| | - Antony N. Davies
- School of Applied Sciences
- Faculty of Computing
- Engineering and Science
- University of South Wales
- UK
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40
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de Raad M, Fischer CR, Northen TR. High-throughput platforms for metabolomics. Curr Opin Chem Biol 2015; 30:7-13. [PMID: 26544850 DOI: 10.1016/j.cbpa.2015.10.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/11/2015] [Indexed: 01/06/2023]
Abstract
Mass spectrometry has become a choice method for broad-spectrum metabolite analysis in both fundamental and applied research. This can range from comprehensive analysis achieved through time-consuming chromatography to the rapid analysis of a few target metabolites without chromatography. In this review article, we highlight current high-throughput MS-based platforms and their potential application in metabolomics. Although current MS platforms can reach throughputs up to 0.5 seconds per sample, the metabolite coverage of these platforms are low compared to low-throughput, separation-based MS methods. High-throughput comes at a cost, as it's a trade-off between sample throughput and metabolite coverage. As we will discuss, promising emerging technologies, including microfluidics and miniaturization of separation techniques, have the potential to achieve both rapid and more comprehensive metabolite analysis.
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Affiliation(s)
- Markus de Raad
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States
| | - Curt R Fischer
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States.
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41
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Sherrod SD, McLean JA. Systems-Wide High-Dimensional Data Acquisition and Informatics Using Structural Mass Spectrometry Strategies. Clin Chem 2015; 62:77-83. [PMID: 26453699 DOI: 10.1373/clinchem.2015.238261] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/12/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND Untargeted multiomics data sets are obtained for samples in systems, synthetic, and chemical biology by integrating chromatographic separations with ion mobility-mass spectrometry (IM-MS) analysis. The data sets are interrogated using bioinformatics strategies to organize the data for identification prioritization. CONTENT The use of big data approaches for data mining of massive data sets in systems-wide analyses is presented. Untargeted biological data across multiomics dimensions are obtained using a variety of chromatography strategies with structural MS. Separation timescales for different techniques and the resulting data deluge when combined with IM-MS are presented. Data mining self-organizing map strategies are used to rapidly filter the data, highlighting those features describing uniqueness to the query. Examples are provided in longitudinal analyses in synthetic biology and human liver exposure to acetaminophen, and in chemical biology for natural product discovery from bacterial biomes. CONCLUSIONS Matching the separation timescales of different forms of chromatography with IM-MS provides sufficient multiomics selectivity to perform untargeted systems-wide analyses. New data mining strategies provide a means for rapidly interrogating these data sets for feature prioritization and discovery in a range of applications in systems, synthetic, and chemical biology.
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Affiliation(s)
- Stacy D Sherrod
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN.
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42
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Baker ES, Burnum-Johnson KE, Ibrahim YM, Orton DJ, Monroe ME, Kelly RT, Moore RJ, Zhang X, Théberge R, Costello CE, Smith RD. Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics 2015; 15:2766-76. [PMID: 26046661 DOI: 10.1002/pmic.201500048] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/06/2015] [Accepted: 06/02/2015] [Indexed: 11/06/2022]
Abstract
Proteomic measurements with greater throughput, sensitivity, and structural information are essential for improving both in-depth characterization of complex mixtures and targeted studies. While LC separation coupled with MS (LC-MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution and rapid structural information has many benefits in proteomic analyses. Technical advances in ion transmission and data acquisition have made ion mobility separations an opportune technology to be easily and effectively incorporated into LC-MS proteomic measurements for enhancing their information content. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.
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Affiliation(s)
- Erin Shammel Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xing Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Roger Théberge
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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43
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Khakinejad M, Kondalaji SG, Tafreshian A, Valentine SJ. Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1115-1127. [PMID: 25895891 DOI: 10.1007/s13361-015-1127-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/26/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H](4+) ions exhibit two major conformer types with collision cross sections of 418 Å(2) and 446 Å(2); the [M + 3H](3+) ions also yield two different conformer types having collision cross sections of 340 Å(2) and 367 Å(2). Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H](3+) ions show faster HDX rate contributions compared with [M + 4H](4+) ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H](4+) ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).
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Affiliation(s)
- Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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44
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Cha J, Burnum-Johnson KE, Bartos A, Li Y, Baker ES, Tilton SC, Webb-Robertson BJM, Piehowski PD, Monroe ME, Jegga AG, Murata S, Hirota Y, Dey SK. Muscle Segment Homeobox Genes Direct Embryonic Diapause by Limiting Inflammation in the Uterus. J Biol Chem 2015; 290:15337-49. [PMID: 25931120 DOI: 10.1074/jbc.m115.655001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 12/30/2022] Open
Abstract
Embryonic diapause is a reproductive strategy widespread in the animal kingdom. This phenomenon is defined by a temporary arrest in blastocyst growth and metabolic activity within a quiescent uterus without implantation until the environmental and maternal milieu become favorable for pregnancy to progress. We found that uterine Msx expression persists during diapause across species; their inactivation in the mouse uterus results in termination of diapause with the development of implantation-like responses ("pseudoimplantation") that ultimately succumbed to resorption. To understand the cause of this failure, we compared proteome profiles between floxed and Msx-deleted uteri. In deleted uteri, several functional networks, including transcription/translation, ubiquitin-proteasome, inflammation, and endoplasmic reticulum stress, were dysregulated. Computational modeling predicted intersection of these pathways on an enhanced inflammatory signature. Further studies showed that this signature was reflected in increased phosphorylated IκB levels and nuclear NFκB in deleted uteri. This was associated with enhanced proteasome activity and endoplasmic reticulum stress. Interestingly, treatment with anti-inflammatory glucocorticoid (dexamethasone) reduced the inflammatory signature with improvement of the diapause phenotype. These findings highlight an unexpected role of uterine Msx in limiting aberrant inflammatory responses to maintain embryonic diapause.
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Affiliation(s)
- Jeeyeon Cha
- From the Division of Reproductive Sciences and
| | - Kristin E Burnum-Johnson
- the Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | | | - Yingju Li
- From the Division of Reproductive Sciences and
| | - Erin S Baker
- the Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Susan C Tilton
- the Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, the Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331
| | | | | | - Matthew E Monroe
- the Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Anil G Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229-3039
| | - Shigeo Murata
- the Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan, and
| | - Yasushi Hirota
- the Department of Obstetrics and Gynecology, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 Japan
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45
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Ewing MA, Conant CRP, Zucker SM, Griffith KJ, Clemmer DE. Selected Overtone Mobility Spectrometry. Anal Chem 2015; 87:5132-8. [DOI: 10.1021/ac504555u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael A. Ewing
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | | | - Steven M. Zucker
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Kent J. Griffith
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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46
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Pan S, Brentnall TA, Chen R. Proteomics analysis of bodily fluids in pancreatic cancer. Proteomics 2015; 15:2705-15. [PMID: 25780901 DOI: 10.1002/pmic.201400476] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/06/2015] [Accepted: 03/13/2015] [Indexed: 12/12/2022]
Abstract
Proteomics study of pancreatic cancer using bodily fluids emphasizes biomarker discovery and clinical application, presenting unique prospect and challenges. Depending on the physiological nature of the bodily fluid and its proximity to pancreatic cancer, the proteomes of bodily fluids, such as pancreatic juice, pancreatic cyst fluid, blood, bile, and urine, can be substantially different in terms of protein constitution and the dynamic range of protein concentration. Thus, a comprehensive discovery and specific detection of cancer-associated proteins within these varied fluids is a complex task, requiring rigorous experiment design and a concerted approach. While major challenges still remain, fluid proteomics studies in pancreatic cancer to date have provided a wealth of information in revealing proteome alterations associated with pancreatic cancer in various bodily fluids.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Ru Chen
- Department of Medicine, University of Washington, Seattle, WA, USA
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47
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Decaris ML, Emson CL, Li K, Gatmaitan M, Luo F, Cattin J, Nakamura C, Holmes WE, Angel TE, Peters MG, Turner SM, Hellerstein MK. Turnover rates of hepatic collagen and circulating collagen-associated proteins in humans with chronic liver disease. PLoS One 2015; 10:e0123311. [PMID: 25909381 PMCID: PMC4409311 DOI: 10.1371/journal.pone.0123311] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/03/2015] [Indexed: 01/08/2023] Open
Abstract
Accumulation and degradation of scar tissue in fibrotic liver disease occur slowly, typically over many years. Direct measurement of fibrogenesis, the rate of scar tissue deposition, may provide valuable therapeutic and prognostic information. We describe here results from a pilot study utilizing in vivo metabolic labeling to measure the turnover rate of hepatic collagen and collagen-associated proteins in plasma for the first time in human subjects. Eight subjects with chronic liver disease were labeled with daily oral doses of 2H2O for up to 8 weeks prior to diagnostic liver biopsy and plasma collection. Tandem mass spectrometry was used to measure the abundance and fractional synthesis rate (FSR) of proteins in liver and blood. Relative protein abundance and FSR data in liver revealed marked differences among subjects. FSRs of hepatic type I and III collagen ranged from 0.2–0.6% per day (half-lives of 4 months to a year) and correlated significantly with worsening histologic fibrosis. Analysis of plasma protein turnover revealed two collagen-associated proteins, lumican and transforming growth factor beta-induced-protein (TGFBI), exhibiting FSRs that correlated significantly with FSRs of hepatic collagen. In summary, this is the first direct measurement of liver collagen turnover in vivo in humans and suggests a high rate of collagen remodeling in advanced fibrosis. In addition, the FSRs of collagen-associated proteins in plasma are measurable and may provide a novel strategy for monitoring hepatic fibrogenesis rates.
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Affiliation(s)
- Martin L. Decaris
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
- * E-mail: (ST); (MD)
| | - Claire L. Emson
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - Kelvin Li
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - Michelle Gatmaitan
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - Flora Luo
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - Jerome Cattin
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - Corelle Nakamura
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - William E. Holmes
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - Thomas E. Angel
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
| | - Marion G. Peters
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, California, United States of America
| | - Scott M. Turner
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
- * E-mail: (ST); (MD)
| | - Marc K. Hellerstein
- Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America
- Department of Nutritional Science and Toxicology, University of California, Berkeley, California, United States of America
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48
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Affiliation(s)
- Jody C. May
- Department
of Chemistry,
Center for Innovative Technology, Vanderbilt Institute for Chemical
Biology, Vanderbilt Institute for Integrative Biosystems Research
and Education , Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department
of Chemistry,
Center for Innovative Technology, Vanderbilt Institute for Chemical
Biology, Vanderbilt Institute for Integrative Biosystems Research
and Education , Vanderbilt University, Nashville, Tennessee 37235, United States
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49
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Ibrahim YM, Baker ES, Danielson WF, Norheim RV, Prior DC, Anderson GA, Belov ME, Smith RD. Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 377:655-662. [PMID: 26185483 PMCID: PMC4501404 DOI: 10.1016/j.ijms.2014.07.034] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A new ion mobility spectrometer (IMS) platform was developed to improve upon the sensitivity and reproducibility of our previous platforms, and further enhance IMS-MS utility for broad 'pan-omics' measurements. The new platform incorporated an improved electrospray ionization source and interface for enhanced sensitivity, and providing the basis for further benefits based upon implementation of multiplexed IMS. The ion optics included electrodynamic ion funnels at both the entrance and exit of the IMS, an ion funnel trap for ion injection, and a design in which nearly all ion optics (e.g. drift rings, ion funnels) were fabricated using printed circuit board technology. The IMS resolving power achieved was ~73 for singly-charged ions, very close to the predicted diffusion-limited resolving power (~75). The platform's performance evaluation (e.g. for proteomics measurements) include LC-IMS-TOF MS datasets for 30 technical replicates for a trypsin digested human serum, and included platform performance in each dimension (LC, IMS and MS) separately.
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Affiliation(s)
- Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
| | - William F Danielson
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
| | - Randolph V Norheim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
| | - David C Prior
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
| | - Gordon A Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
| | - Mikhail E Belov
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352
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May JC, Goodwin CR, McLean JA. Ion mobility-mass spectrometry strategies for untargeted systems, synthetic, and chemical biology. Curr Opin Biotechnol 2014; 31:117-21. [PMID: 25462629 DOI: 10.1016/j.copbio.2014.10.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 12/12/2022]
Abstract
Contemporary strategies that concentrate on only one or a handful of molecular targets limits the utility of the information gained for diagnostic and predictive purposes. Recent advances in the sensitivity, speed, and precision of measurements obtained from ion mobility coupled to mass spectrometry (IM-MS) have accelerated the utility of IM-MS in untargeted, discovery-driven studies in biology. Perhaps most evident is the impact that such wide-scale discovery capabilities have yielded in the areas of systems, synthetic, and chemical biology, where the need for comprehensive, hypothesis-driving studies from multidimensional and unbiased data is required.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Cody R Goodwin
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA.
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