1
|
van der Post S, Seymour RW, Mooradian AD, Held JM. Automating Assignment, Quantitation, and Biological Annotation of Redox Proteomics Datasets with ProteoSushi. Methods Mol Biol 2022; 2399:61-84. [PMID: 35604553 DOI: 10.1007/978-1-0716-1831-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Redox proteomics plays an increasingly important role characterizing the cellular redox state and redox signaling networks. As these datasets grow larger and identify more redox regulated sites in proteins, they provide a systems-wide characterization of redox regulation across cellular organelles and regulatory networks. However, these large proteomic datasets require substantial data processing and analysis in order to fully interpret and comprehend the biological impact of oxidative posttranslational modifications. We therefore developed ProteoSushi, a software tool to biologically annotate and quantify redox proteomics and other modification-specific proteomics datasets. ProteoSushi can be applied to differentially alkylated samples to assay overall cysteine oxidation, chemically labeled samples such as those used to profile the cysteine sulfenome, or any oxidative posttranslational modification on any residue.Here we demonstrate how to use ProteoSushi to analyze a large, public cysteine redox proteomics dataset. ProteoSushi assigns each modified peptide to shared proteins and genes, sums or averages signal intensities for each modified site of interest, and annotates each modified site with the most up-to-date biological information available from UniProt. These biological annotations include known functional roles or modifications of the site, the protein domain(s) that the site resides in, the protein's subcellular location and function, and more.
Collapse
Affiliation(s)
- Sjoerd van der Post
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert W Seymour
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Arshag D Mooradian
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason M Held
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
2
|
Seymour RW, van der Post S, Mooradian AD, Held JM. ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets. J Proteome Res 2021; 20:3621-3628. [PMID: 34056901 DOI: 10.1021/acs.jproteome.1c00203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large-scale proteomic profiling of protein post-translational modifications has provided important insights into the regulation of cell signaling and disease. These modification-specific proteomics workflows nearly universally enrich modified peptides prior to mass spectrometry analysis, but protein-centric proteomic software tools have many limitations evaluating and interpreting these peptide-centric data sets. We, therefore, developed ProteoSushi, a software tool tailored to analysis of each modified site in peptide-centric proteomic data sets that is compatible with any post-translational modification or chemical label. ProteoSushi uses a unique approach to assign identified peptides to shared proteins and genes, minimizing redundancy by prioritizing shared assignments based on UniProt annotation score and optional user-supplied protein/gene lists. ProteoSushi simplifies quantitation by summing or averaging intensities for each modified site, merging overlapping peptide charge states, missed cleavages, spectral matches, and variable modifications into a single value. ProteoSushi also annotates each PTM site with the most up-to-date biological information available from UniProt, such as functional roles or known modifications, the protein domain in which the site resides, the protein's subcellular location and function, and more. ProteoSushi has a graphical user interface for ease of use. ProteoSushi's flexibility and combination of analysis features streamlines peptide-centric data processing and knowledge mining of large modification-specific proteomics data sets.
Collapse
Affiliation(s)
- Robert W Seymour
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Sjoerd van der Post
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States.,Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Arshag D Mooradian
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States.,Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States.,Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
| |
Collapse
|
3
|
Kontostathi G, Makridakis M, Zoidakis J, Vlahou A. Applications of multiple reaction monitoring targeted proteomics assays in human plasma. Expert Rev Mol Diagn 2019; 19:499-515. [PMID: 31057016 DOI: 10.1080/14737159.2019.1615448] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Multiple (or selected) reaction monitoring-mass spectrometry (MRM/SRM) is a targeted proteomic method that can be used for relative and absolute quantification. Multiple reports exist supporting the potential of the approach in proteomic biomarker validation. Areas covered: To get an overview of the applications of MRM in protein quantification in plasma, a search in MedLine/PubMed was performed using the keywords: 'MRM/SRM plasma proteomic/proteomics/proteome'. The retrieved studies were further filtered to focus on disease biomarkers and the main results are summarized. Expert opinion: MRM is increasingly employed for the quantification of both well-established but also newly discovered putative biomarkers and occasionally their post-translationally modified forms in plasma. Fractionation is regularly required for the detection of low abundance proteins. Standardized procedures to facilitate assay establishment and marker quantification have been proposed and, in few cases, implemented. Nevertheless, in most cases, absolute quantification is not performed. To advance, multiple technical issues including the regular use of standard labeled peptides and appropriate quality controls to monitor assay performance should be considered. Additionally, clinical aspects involving careful study design to address biomarker clinical use should also be considered.
Collapse
Affiliation(s)
- Georgia Kontostathi
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Manousos Makridakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Jerome Zoidakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Antonia Vlahou
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| |
Collapse
|
4
|
Rice SJ, Liu X, Zhang J, Belani CP. Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery. Proteomics 2019; 19:e1800135. [DOI: 10.1002/pmic.201800135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/27/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Shawn J. Rice
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Xin Liu
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Jianhong Zhang
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Chandra P. Belani
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
- Department of MedicinePenn State College of Medicine Hershey PA 17033 USA
| |
Collapse
|
5
|
Deng J, Ikenishi F, Smith N, Lazar IM. Streamlined microfluidic analysis of phosphopeptides using stable isotope-labeled synthetic peptides and MRM-MS detection. Electrophoresis 2018; 39:3171-3184. [PMID: 30216485 DOI: 10.1002/elps.201800133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 11/07/2022]
Abstract
Modern high-throughput and high-content biological research is performed with advanced instrumentation and complex and time-consuming protocols, which, as a whole, pose a challenge for routine implementation in a research laboratory. In support of a "bioanalytical toolbox" with potential utility for exploring cellular functions mediated via protein phosphorylation-a post-translational modification (PTM) with essential regulatory roles in a variety of cellular processes-in this work, we describe the development of a simple, integrated microfluidic chip that can perform targeted, quantitative analysis of phosphopeptides involved in cancer-relevant signaling pathways. The microfluidic device comprises microreactors packed with C18 and TiO2 particles for on-chip solid phase extraction (SPE) and phosphopeptide enrichment, and an ESI interface for facilitating multiple reaction monitoring (MRM)-mass spectrometry (MS) detection. The chips are demonstrated for the detection of three phosphopeptides involved in ERBB2/MAPK signaling pathways, selected from the outcome of a proteomic study involving EGF stimulation of SKBR3/HER2+ breast cancer cells. The data demonstrate that the proposed microfluidic strategy can be used for the MS quantification of phosphopeptides in the low nM range from cell lysates without any prior sample pretreatment, fractionation or bioaffinity enrichment, and is generally applicable to the analysis of any phosphopeptide targets.
Collapse
Affiliation(s)
- Jingren Deng
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Fumio Ikenishi
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Nicole Smith
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|
6
|
Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| |
Collapse
|
7
|
Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nat Biotechnol 2017; 35:781-788. [PMID: 28604659 PMCID: PMC5593115 DOI: 10.1038/nbt.3908] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/22/2017] [Indexed: 01/01/2023]
Abstract
Consistent detection and quantification of protein post-translational modifications (PTMs) across sample cohorts is a prerequisite for functional analysis of biological processes. Data-independent acquisition (DIA) is a bottom-up mass spectrometry approach that provides complete information on precursor and fragment ions. However, owing to the convoluted structure of DIA data sets, confident, systematic identification and quantification of peptidoforms has remained challenging. Here, we present inference of peptidoforms (IPF), a fully automated algorithm that uses spectral libraries to query, validate and quantify peptidoforms in DIA data sets. The method was developed on data acquired by the DIA method SWATH-MS and benchmarked using a synthetic phosphopeptide reference data set and phosphopeptide-enriched samples. IPF reduced false site-localization by more than sevenfold compared with previous approaches, while recovering 85.4% of the true signals. Using IPF, we quantified peptidoforms in DIA data acquired from >200 samples of blood plasma of a human twin cohort and assessed the contribution of heritable, environmental and longitudinal effects on their PTMs.
Collapse
Affiliation(s)
- George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Genetics, Stanford University, Stanford, California, USA
| | - Christina Ludwig
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University Munich, Freising, Germany
| | - Alfonso Buil
- Research Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Roskilde, Denmark
| | - Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Martin Soste
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital Campus, London, UK
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Lars Malmström
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,S3IT, University of Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| |
Collapse
|
8
|
Meyer JG, Schilling B. Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques. Expert Rev Proteomics 2017; 14:419-429. [PMID: 28436239 PMCID: PMC5671767 DOI: 10.1080/14789450.2017.1322904] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered: This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e.g., SWATH). Corresponding bioinformatics strategies, as well as application in biological and clinical studies are presented. Expert commentary: Nascent application of highly-multiplexed untargeted DIA, such as SWATH, for accurate protein quantification from clinically relevant and disease-related samples shows great potential to comprehensively investigate biomarker candidates and understand disease.
Collapse
Affiliation(s)
- Jesse G Meyer
- a Mass Spectrometry Core , Buck Institute for Research on Aging , Novato , CA , USA
| | - Birgit Schilling
- a Mass Spectrometry Core , Buck Institute for Research on Aging , Novato , CA , USA
| |
Collapse
|
9
|
Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600278] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Faculty of Sciences and Technology; University of Coimbra; Coimbra Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Institute for Interdisciplinary Research (III); University of Coimbra; Coimbra Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| |
Collapse
|
10
|
Broszczak DA, Sydes ER, Wallace D, Parker TJ. Molecular Aspects of Wound Healing and the Rise of Venous Leg Ulceration: Omics Approaches to Enhance Knowledge and Aid Diagnostic Discovery. Clin Biochem Rev 2017; 38:35-55. [PMID: 28798504 PMCID: PMC5548371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chronic wounds, in particular venous leg ulcers (VLU), represent a substantial burden for economies, healthcare systems and societies worldwide. This burden is exacerbated by the recalcitrant nature of these wounds, despite best practice, evidence-based care, which substantially reduces the quality of life of patients. Furthermore, co-morbidities such as diabetes and cardiovascular disease within ageing populations further contribute to the increasing prevalence in developed countries. This review provides an overview of the literature concerning the cellular and molecular mechanisms of wound healing and aspects where this process fails, resulting in a chronic wound. VLU may arise from chronic venous disease, which presents with many clinical manifestations and can lead to a highly complex disease state. Efforts to comprehend this state using various omics based approaches have delivered some insight into the underlying biology of chronic wounds and revealed markers of differentiation at the genomic, transcriptomic, proteomic and metabolomic levels. Furthermore, this review outlines the array of analytical tools and approaches that have been utilised for capturing multivariate data at each of these molecular levels. Future developments in spatiotemporal analysis of wounds along with the integration of multiple omics datasets may provide much needed information on the key molecules that drive wound chronicity. Such biomarkers have the potential to be developed into clinically relevant diagnostic tools to aid in personalised wound management.
Collapse
Affiliation(s)
- Daniel A Broszczak
- School of Science, Faculty of Health Sciences, Australian Catholic University, Banyo, Qld 4014, Australia
- Tissue Repair and Translational Physiology Program, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4059, Australia
| | - Elizabeth R Sydes
- School of Science, Faculty of Health Sciences, Australian Catholic University, Banyo, Qld 4014, Australia
- Tissue Repair and Translational Physiology Program, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4059, Australia
| | - Daniel Wallace
- Iron and Cancer Research Laboratory, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4059, Australia
| | - Tony J Parker
- Tissue Repair and Translational Physiology Program, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4059, Australia
| |
Collapse
|
11
|
Klement E, Medzihradszky KF. Extracellular Protein Phosphorylation, the Neglected Side of the Modification. Mol Cell Proteomics 2016; 16:1-7. [PMID: 27834735 DOI: 10.1074/mcp.o116.064188] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 11/10/2016] [Indexed: 12/18/2022] Open
Abstract
The very existence of extracellular phosphorylation has been questioned for a long time, although casein phosphorylation was discovered a century ago. In addition, several modification sites localized on secreted proteins or on extracellular or lumenal domains of transmembrane proteins have been catalogued in large scale phosphorylation analyses, though in most such studies this aspect of cellular localization was not considered. Our review presents examples when additional analyses were performed on already public data sets that revealed a wealth of information about this "neglected side" of the modification. We also sum up accumulated knowledge about extracellular phosphorylation, including the discovery of Golgi-residing kinases and the special difficulties encountered in targeted analyses. We hope future phosphorylation studies will not ignore the existence of phosphorylation outside of the cell, and further discoveries will shed more light on its biological role.
Collapse
Affiliation(s)
- Eva Klement
- From the ‡Laboratory of Proteomics Research, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary, and
| | - Katalin F Medzihradszky
- From the ‡Laboratory of Proteomics Research, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary, and .,the §Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, California
| |
Collapse
|
12
|
Schmidlin T, Garrigues L, Lane CS, Mulder TC, van Doorn S, Post H, de Graaf EL, Lemeer S, Heck AJR, Altelaar AFM. Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non-small cell lung cancer. Proteomics 2016; 16:2193-205. [DOI: 10.1002/pmic.201500453] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/12/2016] [Accepted: 05/20/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Thierry Schmidlin
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Luc Garrigues
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | | | - T. Celine Mulder
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Erik L. de Graaf
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
- Current address: Erik L. de Graaf, Fondazione Pisana per la Scienza ONLUS; Via Panfilo Castaldi 2; 56121 Pisa Italy
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - A. F. Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| |
Collapse
|
13
|
Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
Collapse
Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
| |
Collapse
|
14
|
Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich UJ, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized Metal Affinity Chromatography Coupled to Multiple Reaction Monitoring Enables Reproducible Quantification of Phospho-signaling. Mol Cell Proteomics 2015; 15:726-39. [PMID: 26621847 DOI: 10.1074/mcp.o115.054940] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 12/23/2022] Open
Abstract
A major goal in cell signaling research is the quantification of phosphorylation pharmacodynamics following perturbations. Traditional methods of studying cellular phospho-signaling measure one analyte at a time with poor standardization, rendering them inadequate for interrogating network biology and contributing to the irreproducibility of preclinical research. In this study, we test the feasibility of circumventing these issues by coupling immobilized metal affinity chromatography (IMAC)-based enrichment of phosphopeptides with targeted, multiple reaction monitoring (MRM) mass spectrometry to achieve precise, specific, standardized, multiplex quantification of phospho-signaling responses. A multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay targeting phospho-analytes responsive to DNA damage was configured, analytically characterized, and deployed to generate phospho-pharmacodynamic curves from primary and immortalized human cells experiencing genotoxic stress. The multiplexed assays demonstrated linear ranges of ≥3 orders of magnitude, median lower limit of quantification of 0.64 fmol on column, median intra-assay variability of 9.3%, median inter-assay variability of 12.7%, and median total CV of 16.0%. The multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay enabled robust quantification of 107 DNA damage-responsive phosphosites from human cells following DNA damage. The assays have been made publicly available as a resource to the community. The approach is generally applicable, enabling wide interrogation of signaling networks.
Collapse
Affiliation(s)
- Jacob J Kennedy
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Ping Yan
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Lei Zhao
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Richard G Ivey
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Uliana J Voytovich
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Heather D Moore
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Chenwei Lin
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | | | - Derek L Stirewalt
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Kerryn W Reding
- §University of Washington, 1959 NE Pacific St., Seattle, Washington 98195
| | - Jeffrey R Whiteaker
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Amanda G Paulovich
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109;
| |
Collapse
|
15
|
Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 2015; 15:3193-208. [PMID: 26097198 PMCID: PMC4758406 DOI: 10.1002/pmic.201500004] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/27/2015] [Accepted: 06/09/2015] [Indexed: 01/28/2023]
Abstract
Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM-MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.
Collapse
Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alex Root
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| |
Collapse
|
16
|
Sajic T, Liu Y, Aebersold R. Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics Clin Appl 2015; 9:307-21. [PMID: 25504613 DOI: 10.1002/prca.201400117] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/13/2014] [Accepted: 12/10/2014] [Indexed: 12/17/2022]
Abstract
In medicine, there is an urgent need for protein biomarkers in a range of applications that includes diagnostics, disease stratification, and therapeutic decisions. One of the main technologies to address this need is MS, used for protein biomarker discovery and, increasingly, also for protein biomarker validation. Currently, data-dependent analysis (also referred to as shotgun proteomics) and targeted MS, exemplified by SRM, are the most frequently used mass spectrometric methods. Recently developed data-independent acquisition techniques combine the strength of shotgun and targeted proteomics, while avoiding some of the limitations of the respective methods. They provide high-throughput, accurate quantification, and reproducible measurements within a single experimental setup. Here, we describe and review data-independent acquisition strategies and their recent use in clinically oriented studies. In addition, we also provide a detailed guide for the implementation of SWATH-MS (where SWATH is sequential window acquisition of all theoretical mass spectra)-one of the data-independent strategies that have gained wide application of late.
Collapse
Affiliation(s)
- Tatjana Sajic
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | |
Collapse
|