1
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McPherson PAC. Approaches to nonlinear curve fitting in laboratory medicine. Lab Med 2024; 55:111-116. [PMID: 37527550 DOI: 10.1093/labmed/lmad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Nonlinear curve fitting is an important process in laboratory medicine, particularly with the increased use of highly sensitive antibody-based assays. Although the process is often automated in commercially available software, it is important that clinical scientists and physicians recognize the limitations of the various approaches used and are able to select the most appropriate model. This article summarizes the key nonlinear functions and demonstrates their application to common laboratory data. Following this, a basic overview of the statistical comparison of models is presented and then a discussion of important algorithms used in nonlinear curve fitting. An accompanying Microsoft Excel workbook is available that can be used to explore the content of this article.
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Affiliation(s)
- Peter A C McPherson
- Ulster University, School of Pharmacy & Pharmaceutical Science, Coleraine, UK
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2
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Jan S, Mishra AK, Bhat MA, Bhat MA, Jan AT. Pollutants in aquatic system: a frontier perspective of emerging threat and strategies to solve the crisis for safe drinking water. Environ Sci Pollut Res Int 2023; 30:113242-113279. [PMID: 37864686 DOI: 10.1007/s11356-023-30302-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/03/2023] [Indexed: 10/23/2023]
Abstract
Water is an indispensable natural resource and is the most vital substance for the existence of life on earth. However, due to anthropogenic activities, it is being polluted at an alarming rate which has led to serious concern about water shortage across the world. Moreover, toxic contaminants released into water bodies from various industrial and domestic activities negatively affect aquatic and terrestrial organisms and cause serious diseases such as cancer, renal problems, gastroenteritis, diarrhea, and nausea in humans. Therefore, water treatments that can eliminate toxins are very crucial. Unfortunately, pollution treatment remains a difficulty when four broad considerations are taken into account: effectiveness, reusability, environmental friendliness, and affordability. In this situation, protecting water from contamination or creating affordable remedial techniques has become a serious issue. Although traditional wastewater treatment technologies have existed since antiquity, they are both expensive and inefficient. Nowadays, advanced sustainable technical approaches are being created to replace traditional wastewater treatment processes. The present study reviews the sources, toxicity, and possible remediation techniques of the water contaminants.
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Affiliation(s)
- Saima Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, 185234, J&K, India
| | | | - Mujtaba Aamir Bhat
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, 185234, J&K, India
| | - Mudasir Ahmad Bhat
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, 185234, J&K, India
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, 185234, J&K, India.
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3
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Cheng WL, Markus C, Lim CY, Tan RZ, Sethi SK, Loh TP. Calibration Practices in Clinical Mass Spectrometry: Review and Recommendations. Ann Lab Med 2023; 43:5-18. [PMID: 36045052 PMCID: PMC9467832 DOI: 10.3343/alm.2023.43.1.5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/30/2022] [Accepted: 08/18/2022] [Indexed: 12/27/2022] Open
Abstract
Background Calibration is a critical component for the reliability, accuracy, and precision of mass spectrometry measurements. Optimal practice in the construction, evaluation, and implementation of a new calibration curve is often underappreciated. This systematic review examined how calibration practices are applied to liquid chromatography-tandem mass spectrometry measurement procedures. Methods The electronic database PubMed was searched from the date of database inception to April 1, 2022. The search terms used were "calibration," "mass spectrometry," and "regression." Twenty-one articles were identified and included in this review, following evaluation of the titles, abstracts, full text, and reference lists of the search results. Results The use of matrix-matched calibrators and stable isotope-labeled internal standards helps to mitigate the impact of matrix effects. A higher number of calibration standards or replicate measurements improves the mapping of the detector response and hence the accuracy and precision of the regression model. Constructing a calibration curve with each analytical batch recharacterizes the instrument detector but does not reduce the actual variability. The analytical response and measurand concentrations should be considered when constructing a calibration curve, along with subsequent use of quality controls to confirm assay performance. It is important to assess the linearity of the calibration curve by using actual experimental data and appropriate statistics. The heteroscedasticity of the calibration data should be investigated, and appropriate weighting should be applied during regression modeling. Conclusions This review provides an outline and guidance for optimal calibration practices in clinical mass spectrometry laboratories.
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Affiliation(s)
- Wan Ling Cheng
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Corey Markus
- Flinders University International Centre for Point-of-Care Testing, Flinders Health and Medical Research Institute, Flinders University, Adelaide, Australia
| | - Chun Yee Lim
- Engineering Cluster, Singapore Institute of Technology, Singapore, Singapore
| | - Rui Zhen Tan
- Engineering Cluster, Singapore Institute of Technology, Singapore, Singapore
| | - Sunil Kumar Sethi
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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4
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Gotti C, Roux-Dalvai F, Joly-Beauparlant C, Mangnier L, Leclercq M, Droit A. Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard. J Proteome Res 2021; 20:4801-4814. [PMID: 34472865 DOI: 10.1021/acs.jproteome.1c00490] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Over the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins mixture (UPS1-Sigma) at 8 different concentrations in an E. coli proteome background, we tested 36 workflows including 4 different DIA window acquisition schemes and 6 different software tools (DIA-NN, DIA-Umpire, OpenSWATH, ScaffoldDIA, Skyline, and Spectronaut) with or without the use of a DDA spectral library. On the basis of the number of proteins identified, quantification linearity and reproducibility, as well as sensitivity and specificity in 28 pairwise comparisons of different UPS1 concentrations, we summarize the major considerations and propose guidelines for choosing the DIA workflow best suited for LC-MS/MS proteomic analyses. Our 96 DIA raw files and software outputs have been deposited on ProteomeXchange for testing or developing new DIA processing tools.
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Affiliation(s)
- Clarisse Gotti
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Florence Roux-Dalvai
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Charles Joly-Beauparlant
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Loïc Mangnier
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Arnaud Droit
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
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5
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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6
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Lill JR, Mathews WR, Rose CM, Schirle M. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics 2021; 18:503-526. [PMID: 34320887 DOI: 10.1080/14789450.2021.1962300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. AREAS COVERED Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. EXPERT OPINION Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.
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Affiliation(s)
- Jennie R Lill
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - William R Mathews
- OMNI Department, Genentech Inc. 1 DNA Way, South San Francisco, CA, USA
| | - Christopher M Rose
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - Markus Schirle
- Chemical Biology and Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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7
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Martinez Hernandez A, Silbern I, Geffers I, Tatenhorst L, Becker S, Urlaub H, Zweckstetter M, Griesinger C, Eichele G. Low-Expressing Synucleinopathy Mouse Models Based on Oligomer-Forming Mutations and C-Terminal Truncation of α-Synuclein. Front Neurosci 2021; 15:643391. [PMID: 34220415 PMCID: PMC8248494 DOI: 10.3389/fnins.2021.643391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
α-synuclein (αSyn) is the main protein component of Lewy bodies, intracellular inclusions found in the brain of Parkinson's disease (PD) patients. Neurotoxic αSyn species are broadly modified post-translationally and, in patients with genetic forms of PD, carry genetically encoded amino acid substitutions. Mutations and C-terminal truncation can increase αSyn oligomerization and fibrillization. Although several genetic mouse models based on αSyn mutations and/or truncations exist, there is still a lack of mouse models for synucleinopathies not relying on overexpression. We report here two synucleinopathy mouse models, which are based on a triple alanine to proline mutation and a C-terminal truncation of αSyn, but do not overexpress the mutant protein when compared to the endogenous mouse protein. We knocked hαSyn TP or hαSynΔ119 (h stands for "human") into the murine αSyn locus. hαSynTP is a structure-based mutant with triple alanine to proline substitutions that favors oligomers, is neurotoxic and evokes PD-like symptoms in Drosophila melanogaster. hαSynΔ119 lacks 21 amino acids at the C-terminus, favors fibrillary aggregates and occurs in PD. Knocking-in of hαSyn TP or hαSynΔ119 into the murine αSyn locus places the mutant protein under the control of the endogenous regulatory elements while simultaneously disrupting the mαSyn gene. Mass spectrometry revealed that hαSyn TP and hαSynΔ119 mice produced 12 and 10 times less mutant protein, compared to mαSyn in wild type mice. We show phenotypes in 1 and 1.5 years old hαSyn TP and hαSynΔ119 mice, despite the lower levels of hαSynTP and hαSynΔ119 expression. Direct comparison of the two mouse models revealed many commonalities but also aspects unique to each model. Commonalities included strong immunoactive state, impaired olfaction and motor coordination deficits. Neither model showed DAergic neuronal loss. Impaired climbing abilities at 1 year of age and a deviant gait pattern at 1.5 years old were specific for hαSynΔ119 mice, while a compulsive behavior was exclusively detected in hαSyn TP mice starting at 1 year of age. We conclude that even at very moderate levels of expression the two αSyn variants evoke measurable and progressive deficiencies in mutant mice. The two transgenic mouse models can thus be suitable to study αSyn-variant-based pathology in vivo and test new therapeutic approaches.
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Affiliation(s)
- Ana Martinez Hernandez
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ivan Silbern
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Insa Geffers
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Lars Tatenhorst
- Department of Neurology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Stefan Becker
- NMR-Based Structural Biology Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Markus Zweckstetter
- Department of Neurology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany.,NMR-Based Structural Biology Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,German Center for Neurodegenerative Diseases, DZNE, Göttingen, Germany
| | - Christian Griesinger
- Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,NMR-Based Structural Biology Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Gregor Eichele
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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8
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Orsburn BC. Proteome Discoverer-A Community Enhanced Data Processing Suite for Protein Informatics. Proteomes 2021; 9:15. [PMID: 33806881 DOI: 10.3390/proteomes9010015] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 01/01/2023] Open
Abstract
Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers have defaulted to the vendor software Proteome Discoverer. Over the fourteen years since the initial release of the software, it has evolved in parallel with the increasingly complex demands faced by proteomics researchers. Today, Proteome Discoverer exists in two distinct forms with both powerful commercial versions and fully functional free versions in use in many labs today. Throughout the 11 main versions released to date, a central theme of the software has always been the ability to easily view and verify the spectra from which identifications are made. This ability is, even today, a key differentiator from other data analysis solutions. In this review I will attempt to summarize the history and evolution of Proteome Discoverer from its first launch to the versions in use today.
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9
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Savickas S, Kastl P, auf dem Keller U. Combinatorial degradomics: Precision tools to unveil proteolytic processes in biological systems. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2020; 1868:140392. [DOI: 10.1016/j.bbapap.2020.140392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/28/2022]
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10
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Pino LK, Searle BC, Yang HY, Hoofnagle AN, Noble WS, MacCoss MJ. Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics. J Proteome Res 2020; 19:1147-1153. [PMID: 32037841 DOI: 10.1021/acs.jproteome.9b00666] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry is a powerful tool for quantifying protein abundance in complex samples. Advances in sample preparation and the development of data-independent acquisition (DIA) mass spectrometry approaches have increased the number of peptides and proteins measured per sample. Here, we present a series of experiments demonstrating how to assess whether a peptide measurement is quantitative by mass spectrometry. Our results demonstrate that increasing the number of detected peptides in a proteomics experiment does not necessarily result in increased numbers of peptides that can be measured quantitatively.
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Affiliation(s)
- Lindsay K Pino
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Brian C Searle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Han-Yin Yang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.,Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
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11
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Kohl M, Stepath M, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M. CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements. Proteomics 2020; 20:e1900143. [PMID: 32086983 DOI: 10.1002/pmic.201900143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 02/07/2020] [Indexed: 01/29/2023]
Abstract
Targeted proteomics techniques allow accurate quantitative measurements of analytes in complex matrices with dynamic linear ranges that span up to 4-5 orders of magnitude. Hence, targeted methods are promising for the development of robust protein assays in several sensitive areas, for example, in health care. However, exploiting the full method potential requires reliable determination of the dynamic range along with related quantification limits for each analyte. Here, a software named CalibraCurve that enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays is presented. The software uses a variety of measures to assess the accuracy of the calibration, namely precision and trueness. Two different kinds of customizable graphs are created (calibration curves and response factor plots). The accuracy measures and the graphs offer an intuitive, detailed, and reliable opportunity to assess the quality of the model fit. Thus, CalibraCurve is deemed a highly useful and flexible tool to facilitate the development and control of reliable SRM/MRM-MS-based proteomics assays.
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Affiliation(s)
- Michael Kohl
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Markus Stepath
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Thilo Bracht
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Dominik A Megger
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany.,Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, D-45 147, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
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12
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Peshkin L, Gupta M, Ryazanova L, Wühr M. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance. Mol Cell Proteomics 2019; 18:2108-2120. [PMID: 31311848 PMCID: PMC6773559 DOI: 10.1074/mcp.tir119.001317] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 06/11/2019] [Indexed: 01/28/2023] Open
Abstract
Multiplexed proteomics has emerged as a powerful tool to measure relative protein expression levels across multiple conditions. The relative protein abundances are inferred by comparing the signals generated by isobaric tags, which encode the samples' origins. Intuitively, the trust associated with a protein measurement depends on the similarity of ratios from the protein's peptides and the signal-strength of these measurements. However, typically the average peptide ratio is reported as the estimate of relative protein abundance, which is only the most likely ratio with a very naive model. Moreover, there is no sense on the confidence in these measurements. Here, we present a mathematically rigorous approach that integrates peptide signal strengths and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence (BACIQ). The main advantages of BACIQ are: (1) It removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; (2) Confidence can be assigned without replicates; (3) For repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; (4) For repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. To demonstrate the power of BACIQ we reanalyzed previously published data on subcellular protein movement on treatment with an Exportin-1 inhibiting drug. We detect ∼2× more highly significant movers, down to subcellular localization changes of ∼1%. Thus, our method drastically increases the value obtainable from quantitative proteomics experiments, helping researchers to interpret their data and prioritize resources. To make our approach easily accessible we distribute it via a Python/Stan package.
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Affiliation(s)
- Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Meera Gupta
- Department of Molecular Biology & the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton, NJ 08544
| | - Lillia Ryazanova
- Department of Molecular Biology & the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton, NJ 08544
| | - Martin Wühr
- Department of Molecular Biology & the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton, NJ 08544.
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13
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Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ. Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. J Am Soc Mass Spectrom 2019; 30:669-684. [PMID: 30671891 PMCID: PMC6445824 DOI: 10.1007/s13361-018-2122-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 05/22/2023]
Abstract
A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data-independent acquisition (DIA) approaches that acquire MS/MS spectra independently of precursor information have been developed to overcome the reproducibility challenges of data-dependent acquisition and the limited breadth of targeted proteomics strategies. Typical DIA implementations use wide MS/MS isolation windows to acquire comprehensive fragment ion data. However, wide isolation windows produce highly chimeric spectra, limiting the achievable sensitivity and accuracy of quantification and identification. Here, we present a DIA strategy in which spectra are collected with overlapping (rather than adjacent or random) windows and then computationally demultiplexed. This approach improves precursor selectivity by nearly a factor of 2, without incurring any loss in mass range, mass resolution, chromatographic resolution, scan speed, or other key acquisition parameters. We demonstrate a 64% improvement in sensitivity and a 17% improvement in peptides detected in a 6-protein bovine mix spiked into a yeast background. To confirm the method's applicability to a realistic biological experiment, we also analyze the regulation of the proteasome in yeast grown in rapamycin and show that DIA experiments with overlapping windows can help elucidate its adaptation toward the degradation of oxidatively damaged proteins. Our integrated computational and experimental DIA strategy is compatible with any DIA-capable instrument. The computational demultiplexing algorithm required to analyze the data has been made available as part of the open-source proteomics software tools Skyline and msconvert (Proteowizard), making it easy to apply as part of standard proteomics workflows. Graphical Abstract.
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Affiliation(s)
- Dario Amodei
- Department of Radiology, Stanford University, 3155 Porter Drive, Palo Alto, CA USA
| | - Jarrett Egertson
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Austin Keller
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Don Marsh
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Olga Vitek
- College of Computer and Information Science, Northeastern University, 440 Huntington Ave, Boston, MA USA
| | - Parag Mallick
- Department of Radiology, Stanford University, 3155 Porter Drive, Palo Alto, CA USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
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Chiva C, Pastor O, Trilla-Fuertes L, Gámez-Pozo A, Fresno Vara JÁ, Sabidó E. Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice. Anal Chem 2019; 91:4934-4938. [DOI: 10.1021/acs.analchem.8b05802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Olga Pastor
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | | | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, C/Faraday 7, 28049, Madrid, Spain
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
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