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King CD, Kapp KL, Arul AB, Choi MJ, Robinson RAS. Advancements in automation for plasma proteomics sample preparation. Mol Omics 2022; 18:828-839. [PMID: 36048090 PMCID: PMC9879274 DOI: 10.1039/d2mo00122e] [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] [Indexed: 01/28/2023]
Abstract
Automation is necessary to increase sample processing throughput for large-scale clinical analyses. Replacement of manual pipettes with robotic liquid handler systems is especially helpful in processing blood-based samples, such as plasma and serum. These samples are very heterogenous, and protein expression can vary greatly from sample-to-sample, even for healthy controls. Detection of true biological changes requires that variation from sample preparation steps and downstream analytical detection methods, such as mass spectrometry, remains low. In this mini-review, we discuss plasma proteomics protocols and the benefits of automation towards enabling detection of low abundant proteins and providing low sample error and increased sample throughput. This discussion includes considerations for automation of major sample depletion and/or enrichment strategies for plasma toward mass spectrometry detection.
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Affiliation(s)
- Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, USA
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2
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Navajas R, Corrales F, Paradela A. Quantitative proteomics-based analyses performed on pre-eclampsia samples in the 2004-2020 period: a systematic review. Clin Proteomics 2021; 18:6. [PMID: 33499801 PMCID: PMC7836571 DOI: 10.1186/s12014-021-09313-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Quantitative proteomics is an invaluable tool in biomedicine for the massive comparative analysis of protein component of complex biological samples. In the last two decades, this technique has been used to describe proteins potentially involved in the pathophysiological mechanisms of preeclampsia as well as to identify protein biomarkers that could be used with diagnostic/prognostic purposes in pre-eclampsia. RESULTS We have done a systematic review of all proteomics-based papers describing differentially expressed proteins in this disease. Searching Pubmed with the terms pre-eclampsia and proteomics, restricted to the Title/Abstract and to MeSH fields, and following manual curation of the original list, retrieved 69 original articles corresponding to the 2004-2020 period. We have only considered those results based on quantitative, unbiased proteomics studies conducted in a controlled manner on a cohort of control and pre-eclamptic individuals. The sources of biological material used were serum/plasma (n = 32), placenta (n = 23), urine (n = 9), cerebrospinal fluid (n = 2), amniotic fluid (n = 2) and decidual tissue (n = 1). Overall results were filtered based on two complementary criteria. First, we have only accounted all those proteins described in at least two (urine), three (placenta) and four (serum/plasma) independent studies. Secondly, we considered the consistency of the quantitative data, that is, inter-study agreement in the protein abundance control/pre-eclamptic ratio. The total number of differential proteins in serum/plasma (n = 559), placenta (n = 912), urine (n = 132) and other sources of biological material (n = 26), reached 1631 proteins. Data were highly complementary among studies, resulting from differences on biological sources, sampling strategies, patient stratification, quantitative proteomic analysis methods and statistical data analysis. Therefore, stringent filtering was applied to end up with a cluster of 18, 29 and 16 proteins consistently regulated in pre-eclampsia in placenta, serum/plasma and urine, respectively. The systematic collection, standardization and evaluation of the results, using diverse filtering criteria, provided a panel of 63 proteins whose levels are consistently modified in the context of pre-eclampsia.
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Affiliation(s)
- Rosana Navajas
- Functional Proteomics Facility, Centro Nacional de Biotecnología (CNB-CSIC), ProteoRed-ISCIII, Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Facility, Centro Nacional de Biotecnología (CNB-CSIC), ProteoRed-ISCIII, Madrid, Spain
| | - Alberto Paradela
- Functional Proteomics Facility, Centro Nacional de Biotecnología (CNB-CSIC), ProteoRed-ISCIII, Madrid, Spain.
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3
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Maia T, Staes A, Plasman K, Pauwels J, Boucher K, Argentini A, Martens L, Montoye T, Gevaert K, Impens F. Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control. ACS OMEGA 2020; 5:6754-6762. [PMID: 32258910 PMCID: PMC7114614 DOI: 10.1021/acsomega.0c00080] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along with the sample preparation protocol, in particular, after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in the MS-loading solvent, consuming only 2 μL of sample. We compared the performance of the microfluidic spectrophotometer with a standard device and determined the optimal sample amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. A careful evaluation of selected LC and MS parameters allowed us to define 3 μg as an optimal peptide amount to be injected into this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells and showing that injecting equal peptide amounts, rather than approximate ones, result in less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control.
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Affiliation(s)
- Teresa
Mendes Maia
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- VIB
Proteomics Core, Albert
Baertsoenkaai 3, Ghent 9000, Belgium
| | - An Staes
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- VIB
Proteomics Core, Albert
Baertsoenkaai 3, Ghent 9000, Belgium
| | - Kim Plasman
- Alzheimer
Research Foundation, Kalkhoevestraat 1, Waregem 8790, Belgium
| | - Jarne Pauwels
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- VIB
Proteomics Core, Albert
Baertsoenkaai 3, Ghent 9000, Belgium
| | - Katie Boucher
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- VIB
Proteomics Core, Albert
Baertsoenkaai 3, Ghent 9000, Belgium
| | - Andrea Argentini
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Bioinformatics
Institute Ghent, Ghent University, Ghent 9000, Belgium
| | - Lennart Martens
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Bioinformatics
Institute Ghent, Ghent University, Ghent 9000, Belgium
| | - Tony Montoye
- Business
Development Management, VIB, Ghent 9000, Belgium
| | - Kris Gevaert
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
| | - Francis Impens
- VIB
Center for Medical Biotechnology, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- VIB
Proteomics Core, Albert
Baertsoenkaai 3, Ghent 9000, Belgium
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Yokota H. Applications of proteomics in pharmaceutical research and development. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:17-21. [PMID: 29753086 DOI: 10.1016/j.bbapap.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/10/2018] [Accepted: 05/08/2018] [Indexed: 01/13/2023]
Abstract
The significance of proteomics in the pharmaceutical industry has increased since overcoming initial difficulties. This review discusses recent proteomics publications from pharmaceutical companies to identify new trends in proteomics applications to research and development. Applications of proteomics such as chemical proteomics, protein expression profiling, targeted protein quantitation, analysis of protein-protein interactions and post-translational modification are widely used by various sections of the industry. Technological advancements in proteomics will further accelerate pharmaceutical research and development.
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Affiliation(s)
- Hiroyuki Yokota
- Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba-shi 305-8585, Japan.
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Kim H, Park J, Wang JI, Kim Y. Recent advances in proteomic profiling of pancreatic ductal adenocarcinoma and the road ahead. Expert Rev Proteomics 2017; 14:963-971. [PMID: 28926720 DOI: 10.1080/14789450.2017.1382356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide. However, there remain many unmet clinical needs, from diagnosis to treatment strategies. The inherent complexity of the molecular characteristics of PDAC has made it difficult to meet these challenges, rendering proteomic profiling of PDAC a critical area of research. Area covered: In this review, we present recent advances in mass spectrometry (MS) and its current application in proteomic studies on PDAC. In addition, we discuss future directions for research that can efficiently incorporate current MS-based technologies that address key issues of PDAC proteomics. Expert commentary: Compared with other cancer studies, little progress has been made in PDAC proteomics, perhaps attributed to the difficulty in performing in-depth and large-scale clinical studies on PDAC. However, recent advances in mass spectrometry can advance PDAC proteomics past the fundamental research stage.
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Affiliation(s)
- Hyunsoo Kim
- a Department of Biomedical Sciences , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,c Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Joonho Park
- b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Joseph I Wang
- b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Youngsoo Kim
- a Department of Biomedical Sciences , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,c Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
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Zhu M, Zhang P, Geng-Spyropoulos M, Moaddel R, Semba RD, Ferrucci L. A robotic protocol for high-throughput processing of samples for selected reaction monitoring assays. Proteomics 2016; 17. [PMID: 27862927 DOI: 10.1002/pmic.201600339] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/19/2016] [Accepted: 11/11/2016] [Indexed: 11/10/2022]
Abstract
Selected reaction monitoring mass spectrometry (SRM-MS) is a sensitive and accurate method for the quantification of targeted proteins in biological specimens. However, the sample throughput and reliability of this technique is limited by the complexity of sample preparation, as well as instrumentation and data processing. Modern robotic equipment allows for rapid and accurate processing of large number of samples and makes SRM-MS assay applicable in epidemiological studies. Herein, we describe an automated sample processing platform developed in the context of an SRM-MS protocol for the assay of complement factor H protein and its variants in human plasma. We report detailed performance data on plasma digestion, sample cleanup and optimized robotic handling implemented on a Biomek® NXp Workstation. Method validation was assessed with isotopically labeled peptide standards and had high reproducibility of intra-day assay (CVs from 2.7 to 17.5% with median CV of 5.3%) and inter-day assay (CVs from 4.8 to 17.6 with median CV of 7.2%) for all peptides.
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Affiliation(s)
- Min Zhu
- National Institute on Aging, Baltimore, MD, USA
| | - Pingbo Zhang
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Najam-ul-Haq M, Jabeen F, Shafiq F, Sajid S, Saba A. New cellulose–silica composite IMAC/C18 for the selective enrichment of phosphorylated molecules and the improved recovery of hydrophilic species. RSC Adv 2015. [DOI: 10.1039/c4ra10254a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new methodology is reported for the synthesis of a hydrophilic cellulose–silica composite, followed by derivatization for the selective enrichment of phosphopeptides and use as a desalting material prior to mass spectrometric analysis.
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Affiliation(s)
- Muhammad Najam-ul-Haq
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Fahmida Jabeen
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Faiza Shafiq
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Salman Sajid
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Ambreen Saba
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
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Micro-scale strategy to detect spermine and spermidine by MALDI-TOF MS in foods and identification of apoptosis-related proteins by nano-flow UPLC-MS/MS after treatment with spermine and spermidine. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 978-979:131-7. [PMID: 25541472 DOI: 10.1016/j.jchromb.2014.11.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 11/16/2014] [Accepted: 11/29/2014] [Indexed: 11/20/2022]
Abstract
Spermine and spermidine are multiple-nitrogen compounds found in many foods. Both compounds are essential for cell growth and human health. This study established a simple and fast method of detecting spermine and spermidine in food samples by matrix-assisted laser desorption/ionization combined with time-of-flight mass spectrometry (MALDI-TOF MS). After a simple sample preparation procedure, spermine and spermidine were directly detected by MALDI-TOF MS with no additional purification procedure. The calibration curves for spermine and spermidine ranged from 0.1 to 10 μg/mL. In intra- and inter-batch assays of three different concentrations of spermine and spermidine, all relative standard deviations and relative errors were below 18.9%. These experimental results confirmed the practicability and effectiveness of the proposed MALDI-TOF MS method for fast determination of spermine and spermidine in food samples. Furthermore, since spermine and spermidine have important roles in apoptosis, up-regulation and down-regulation of spermine and spermidine during apoptosis were analyzed. After treating NRK-52E cells with spermine and spermidine, the cells were lysed, and cell proteins were collected, and digested. Apoptosis-related proteins were then identified by tandem MS.
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