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Gao Y, Kim H, Kitata RB, Lin TT, Swensen AC, Shi T, Liu T. Multiplexed quantitative proteomics in prostate cancer biomarker development. Adv Cancer Res 2024; 161:31-69. [PMID: 39032952 DOI: 10.1016/bs.acr.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Prostate cancer (PCa) is the most common non-skin cancer among men in the United States. However, the widely used protein biomarker in PCa, prostate-specific antigen (PSA), while useful for initial detection, its use alone cannot detect aggressive PCa and can lead to overtreatment. This chapter provides an overview of PCa protein biomarker development. It reviews the state-of-the-art liquid chromatography-mass spectrometry-based proteomics technologies for PCa biomarker development, such as enhancing the detection sensitivity of low-abundance proteins through antibody-based or antibody-independent protein/peptide enrichment, enriching post-translational modifications such as glycosylation as well as information-rich extracellular vesicles, and increasing accuracy and throughput using advanced data acquisition methodologies. This chapter also summarizes recent PCa biomarker validation studies that applied those techniques in diverse specimen types, including cell lines, tissues, proximal fluids, urine, and blood, developing novel protein biomarkers for various clinical applications, including early detection and diagnosis, prognosis, and therapeutic intervention of PCa.
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Affiliation(s)
- Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hyeyoon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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Sharmeen S, Suh K, Kyei I, Jones J, Olupathage H, Campbell A, Hage DS. Immunoaffinity Chromatography for Protein Purification and Analysis. Curr Protoc 2023; 3:e867. [PMID: 37610261 DOI: 10.1002/cpz1.867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Immunoaffinity chromatography (IAC) is a type of liquid chromatography that uses immobilized antibodies or related binding agents as selective stationary phases for sample separation or analysis. The strong binding and high selectivity of antibodies have made IAC a popular tool for the purification and analysis of many chemicals and biochemicals, including proteins. The basic principles of IAC are described as related to the use of this method for protein purification and analysis. The main factors to consider in this technique are also presented under a discussion of the general strategy to follow during the development of a new IAC method. Protocols, as illustrated using human serum albumin (HSA) as a model protein, are provided for the use of IAC in several formats. This includes both the use of IAC with traditional low-performance supports such as agarose for off-line immunoextraction and supports used in high-performance IAC for on-line immunoextraction. The use of IAC for protein analysis as a flow-based or chromatographic immunoassay is also discussed and described using HSA and a competitive binding assay format as an example. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Off-line immunoextraction by traditional immunoaffinity chromatography Basic Protocol 2: On-line immunoextraction by high-performance immunoaffinity chromatography Basic Protocol 3: Competitive binding chromatographic immunoassay.
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Affiliation(s)
- Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Jacob Jones
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | | | - Avery Campbell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Gao Y, Wang YT, Chen Y, Wang H, Young D, Shi T, Song Y, Schepmoes AA, Kuo C, Fillmore TL, Qian WJ, Smith RD, Srivastava S, Kagan J, Dobi A, Sesterhenn IA, Rosner IL, Petrovics G, Rodland KD, Srivastava S, Cullen J, Liu T. Proteomic Tissue-Based Classifier for Early Prediction of Prostate Cancer Progression. Cancers (Basel) 2020; 12:cancers12051268. [PMID: 32429558 PMCID: PMC7281161 DOI: 10.3390/cancers12051268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 01/17/2023] Open
Abstract
Although ~40% of screen-detected prostate cancers (PCa) are indolent, advanced-stage PCa is a lethal disease with 5-year survival rates around 29%. Identification of biomarkers for early detection of aggressive disease is a key challenge. Starting with 52 candidate biomarkers, selected from existing PCa genomics datasets and known PCa driver genes, we used targeted mass spectrometry to quantify proteins that significantly differed in primary tumors from PCa patients treated with radical prostatectomy (RP) across three study outcomes: (i) metastasis ≥1-year post-RP, (ii) biochemical recurrence ≥1-year post-RP, and (iii) no progression after ≥10 years post-RP. Sixteen proteins that differed significantly in an initial set of 105 samples were evaluated in the entire cohort (n = 338). A five-protein classifier which combined FOLH1, KLK3, TGFB1, SPARC, and CAMKK2 with existing clinical and pathological standard of care variables demonstrated significant improvement in predicting distant metastasis, achieving an area under the receiver-operating characteristic curve of 0.92 (0.86, 0.99, p = 0.001) and a negative predictive value of 92% in the training/testing analysis. This classifier has the potential to stratify patients based on risk of aggressive, metastatic PCa that will require early intervention compared to low risk patients who could be managed through active surveillance.
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Affiliation(s)
- Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Yongmei Chen
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Hui Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Denise Young
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Yingjie Song
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Athena A. Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Claire Kuo
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Thomas L. Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA; (S.S.); (J.K.)
| | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA; (S.S.); (J.K.)
| | - Albert Dobi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | | | - Inger L. Rosner
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Gyorgy Petrovics
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, USA
- Correspondence: (K.D.R.); (J.C.); (T.L.)
| | - Shiv Srivastava
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Jennifer Cullen
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (K.D.R.); (J.C.); (T.L.)
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
- Correspondence: (K.D.R.); (J.C.); (T.L.)
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Sobsey CA, Ibrahim S, Richard VR, Gaspar V, Mitsa G, Lacasse V, Zahedi RP, Batist G, Borchers CH. Targeted and Untargeted Proteomics Approaches in Biomarker Development. Proteomics 2020; 20:e1900029. [DOI: 10.1002/pmic.201900029] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/10/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Constance A. Sobsey
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vincent R. Richard
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vanessa Gaspar
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Georgia Mitsa
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vincent Lacasse
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - René P. Zahedi
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Gerald Batist
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill University Montreal Quebec H4A 3T2 Canada
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill University Montreal Quebec H4A 3T2 Canada
- Department of Data Intensive Science and EngineeringSkolkovo Institute of Science and TechnologySkolkovo Innovation Center Moscow 143026 Russia
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A new paradigm in public health assessment: Water fingerprinting for protein markers of public health using mass spectrometry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115621] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Matsumoto M, Nakayama KI. The promise of targeted proteomics for quantitative network biology. Curr Opin Biotechnol 2018; 54:88-97. [PMID: 29550704 DOI: 10.1016/j.copbio.2018.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/21/2018] [Accepted: 02/27/2018] [Indexed: 12/20/2022]
Abstract
Proteomics is a powerful tool for obtaining information on a large number of proteins with regard to their expression levels, interactions with other molecules, and posttranslational modifications. Whereas nontargeted, discovery proteomics uncovers differences in the proteomic landscape under different conditions, targeted proteomics has been developed to overcome the limitations of this approach with regard to quantitation. In addition to technical advances in instruments and informatics tools, the advent of the synthetic proteome composed of synthetic peptides or recombinant proteins has advanced the adoption of targeted proteomics across a wide range of research fields. Targeted proteomics can now be applied to measurement of the dynamics of any proteins of interest under a variety of conditions as well as to estimation of the absolute abundance or stoichiometry of proteins in a given network. Multiplexed targeted proteomics assays of high reproducibility and accuracy can provide insight at the quantitative level into entire networks that govern biological phenomena or diseases. Such assays will establish a new paradigm for data-driven science.
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Affiliation(s)
- Masaki Matsumoto
- Department of Molecular and Cellular Biology and Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology and Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
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An ultrasensitive aptasensor for prostate specific antigen assay based on Exonuclease T-aided cyclic cleavage. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9203-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Silva LM, Clements JA. Mass spectrometry based proteomics analyses in kallikrein-related peptidase research: implications for cancer research and therapy. Expert Rev Proteomics 2017; 14:1119-1130. [PMID: 29025353 DOI: 10.1080/14789450.2017.1389637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Kallikrein-related peptidases (KLKs) are a family of serine peptidases that are deregulated in numerous pathological conditions, with a multitude of KLK-mediated functional roles implicated in the progression of cancer. Advances in multidimensional mass spectrometry (MS)-based proteomics have facilitated the quantitative measurement of deregulated KLK expression in cancer, identifying certain KLKs, as well as their substrates, as potential cancer biomarkers. Areas covered: In this review, we discuss how these approaches have been utilized for KLK biomarker discovery and unbiased substrate determination in complex protein pools that mimic the in vivo extracellular microenvironment. Expert commentary: Although a limited number of studies have been performed, the quantity of information generated has greatly improved our understanding of the functional roles of KLKs in cancer progression. In addition, these data suggest additional means through which deregulated KLK expression may be targeted in cancer treatment, highlighting the potential therapeutic value of these state-of-the-art MS-based studies.
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Affiliation(s)
- Lakmali Munasinghage Silva
- a Proteases and Tissue Remodeling Section, Oral and Pharyngeal Cancer Branch , National Institute of Dental and Craniofacial Research, National Institutes of Health , Bethesda , MD , USA
| | - Judith Ann Clements
- b School of Biomedical Sciences , Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology (QUT), Translational Research Institute , Woolloongabba , Australia
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10
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Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. Sci Data 2017; 4:170091. [PMID: 28722704 PMCID: PMC5516542 DOI: 10.1038/sdata.2017.91] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 06/01/2017] [Indexed: 02/06/2023] Open
Abstract
Mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are emerging as a promising tool for verification of candidate proteins in biological and biomedical applications. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large sets of targeted MS-based assays, and a depository to share assays publicly. Herein, we report the development of 98 SRM assays that have been thoroughly characterized according to the CPTAC Assay Characterization Guidance Document; 37 of these passed all five experimental tests. The assays cover 70 proteins previously identified at the protein level in ovarian tumors. The experiments, methods and results for characterizing these SRM assays for their MS response, repeatability, selectivity, stability, and endogenous detection are described in detail. Data are available via PeptideAtlas, Panorama and the CPTAC Assay Portal.
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Yang J, Tang A, Zhang S, Sun X, Ming L. The age-specific reference intervals for tPSA, fPSA, and %fPSA in healthy Han ethnic male. J Clin Lab Anal 2016; 31. [PMID: 27645821 DOI: 10.1002/jcla.22062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Prostate cancer (PC) is one of the most common malignancies in male, and has become the fastest growing malignancy in recent years. Prostate specific antigen (PSA) is widely used as a tumor marker to screen for PC. Many studies have been performed to define the reference intervals (RIs) for total circulating PSA (tPSA). The results were different among different nations and races, even in the same race. Few researches have been performed on the RIs of free PSA (fPSA) and the ratio of free to total PSA (%fPSA). In this study, we aimed to simultaneously determine the age-specific RIs for tPSA, fPSA, and %fPSA in the healthy Han ethnic male. METHODS A total of 1862 apparently healthy male aged from 21 to 94 years were included in our study. Nonparametric 95th percentile intervals were used to define the RIs. RESULTS The reference limits in different age groups (21-50, 51-60, 61-70, 71-80, and ≥81 years) were 2.07, 3.59, 4.93, 6.83, and 7.73 ng/mL for tPSA, and 0.60, 0.76, 0.83, 1.30, and 2.41 ng/mL for fPSA. The RIs of %fPSA were ≥0.16 for 21-50 years and ≥0.13 for male over 50 years old. CONCLUSIONS We established age-specific RIs for tPSA, fPSA and %fPSA. The newly established RIs should be more suitable for Chinese Han ethnic male. It will be valuable for physicians to make exact medical decision and appropriate medical intervention.
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Affiliation(s)
- Jingjing Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory Medicine of Henan provinces, Zhengzhou, Henan, China
| | - Aiguo Tang
- Department of Clinical Laboratory, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shijie Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory Medicine of Henan provinces, Zhengzhou, Henan, China
| | - Xiaoxu Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory Medicine of Henan provinces, Zhengzhou, Henan, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory Medicine of Henan provinces, Zhengzhou, Henan, China
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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13
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Yang YC, Tseng WL. 1,4-Benzenediboronic-Acid-Induced Aggregation of Gold Nanoparticles: Application to Hydrogen Peroxide Detection and Biotin-Avidin-Mediated Immunoassay with Naked-Eye Detection. Anal Chem 2016; 88:5355-62. [PMID: 27091002 DOI: 10.1021/acs.analchem.6b00668] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hydrogen-peroxide (H2O2)-induced growth of small-sized gold nanoparticles (AuNPs) is often implemented for H2O2 sensing and plasmonic immunoassay. In contrast, there is little-to-no information in the literature regarding the application of H2O2-inhibited aggregation of citrate-capped AuNPs. This study discloses that benzene-1,4-diboronic acid (BDBA) was effective in driving the aggregation of citrate-capped AuNPs through an interaction between α-hydroxycarboxylate of citrate and boronic acids of BDBA. The H2O2-mediated oxidation of BDBA resulted in the conversion of boronic acid groups to phenol groups. The oxidized BDBA was incapable of triggering the aggregation of citrate-capped AuNPs. Thus, the presence of H2O2 prohibited BDBA-induced aggregation of citrate-capped AuNPs. The BDBA-induced aggregation of citrate-capped AuNPs can be paired with the glucose oxidase (GOx)-glucose system to design a colorimetric probe for glucose. Moreover, a H2O2·BDBA·AuNP probe was integrated with sandwich immunoassay, biotinylated antibody, and avidin-conjugated GOx for the selective naked-eye detection of rabbit immunoglobulin G (IgG) and human-prostate-specific antigen (PSA). The lowest detectable concentrations of rabbit IgG and human PSA by the naked eye were down to 0.1 and 4 ng/mL, respectively. More importantly, the proposed plasmonic immunoassay allowed the naked-eye quantification of 0-10 ng/mL PSA at an interval of 2 ng/mL in plasma samples.
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Affiliation(s)
- Ya-Chun Yang
- Department of Chemistry, National Sun Yat-sen University , Kaohsiung 80424, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, National Sun Yat-sen University , Kaohsiung 80424, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University , Kaohsiung 80708, Taiwan.,Center for Nanoscience and Nanotechnology, National Sun Yat-sen University , Kaohsiung 80424, Taiwan
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14
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Sabbagh B, Mindt S, Neumaier M, Findeisen P. Clinical applications of MS-based protein quantification. Proteomics Clin Appl 2016; 10:323-45. [DOI: 10.1002/prca.201500116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/18/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Bassel Sabbagh
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Sonani Mindt
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
- MVZ Labor Dr. Limbach und Kollegen; Heidelberg Germany
- Working Group Proteomics of the German United Society for Clinical Chemistry and Laboratory Medicine e.V. (DGKL); Bonn Germany
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15
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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.
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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.
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16
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Percy AJ, Yang J, Chambers AG, Borchers CH. Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards. Methods Mol Biol 2016; 1410:1-21. [PMID: 26867735 DOI: 10.1007/978-1-4939-3524-6_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Absolute quantitative strategies are emerging as a powerful and preferable means of deriving concentrations in biological samples for systems biology applications. Method development is driven by the need to establish new-and validate current-protein biomarkers of high-to-low abundance for clinical utility. In this chapter, we describe a methodology involving two-dimensional (2D) reversed-phase liquid chromatography (RPLC), operated under alkaline and acidic pH conditions, combined with multiple reaction monitoring (MRM)-mass spectrometry (MS) (also called selected reaction monitoring (SRM)-MS) and a complex mixture of stable isotope-labeled standard (SIS) peptides, to quantify a broad and diverse panel of 253 proteins in human blood plasma. The quantitation range spans 8 orders of magnitude-from 15 mg/mL (for vitamin D-binding protein) to 450 pg/mL (for protein S100-B)-and includes 31 low-abundance proteins (defined as being <10 ng/mL) of potential disease relevance. The method is designed to assess candidates at the discovery and/or verification phases of the biomarker pipeline and can be adapted to examine smaller or alternate panels of proteins for higher sample throughput. Also detailed here is the application of our recently developed software tool-Qualis-SIS-for protein quantitation (via regression analysis of standard curves) and quality assessment of the resulting data. Overall, this chapter provides the blueprint for the replication of this quantitative proteomic method by proteomic scientists of all skill levels.
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Affiliation(s)
- Andrew J Percy
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada.
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Andrew G Chambers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada.
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada.
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17
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Percy AJ, Yang J, Chambers AG, Mohammed Y, Miliotis T, Borchers CH. Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:515-530. [DOI: 10.1007/978-3-319-41448-5_24] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Wang H, Shi T, Qian WJ, Liu T, Kagan J, Srivastava S, Smith RD, Rodland KD, Camp DG. The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification. Expert Rev Proteomics 2015; 13:99-114. [PMID: 26581546 DOI: 10.1586/14789450.2016.1122529] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS) -based proteomics has become an indispensable tool with broad applications in systems biology and biomedical research. With recent advances in liquid chromatography (LC) and MS instrumentation, LC-MS is making increasingly significant contributions to clinical applications, especially in the area of cancer biomarker discovery and verification. To overcome challenges associated with analyses of clinical samples (for example, a wide dynamic range of protein concentrations in bodily fluids and the need to perform high throughput and accurate quantification of candidate biomarker proteins), significant efforts have been devoted to improve the overall performance of LC-MS-based clinical proteomics platforms. Reviewed here are the recent advances in LC-MS and its applications in cancer biomarker discovery and quantification, along with the potentials, limitations and future perspectives.
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Affiliation(s)
- Hui Wang
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tujin Shi
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tao Liu
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Jacob Kagan
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Sudhir Srivastava
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Richard D Smith
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Karin D Rodland
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - David G Camp
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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19
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Pernikářová V, Bouchal P. Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps. Expert Rev Proteomics 2015; 12:651-67. [PMID: 26456120 DOI: 10.1586/14789450.2015.1094381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The concept of personalized medicine includes novel protein biomarkers that are expected to improve the early detection, diagnosis and therapy monitoring of malignant diseases. Tissues, biofluids, cell lines and xenograft models are the common sources of biomarker candidates that require verification of clinical value in independent patient cohorts. Targeted proteomics - based on selected reaction monitoring, or data extraction from data-independent acquisition based digital maps - now represents a promising mass spectrometry alternative to immunochemical methods. To date, it has been successfully used in a high number of studies answering clinical questions on solid malignancies: breast, colorectal, prostate, ovarian, endometrial, pancreatic, hepatocellular, lung, bladder and others. It plays an important role in functional proteomic experiments that include studying the role of post-translational modifications in cancer progression. This review summarizes verified biomarker candidates successfully quantified by targeted proteomics in this field and directs the readers who plan to design their own hypothesis-driven experiments to appropriate sources of methods and knowledge.
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Affiliation(s)
- Vendula Pernikářová
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic
| | - Pavel Bouchal
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic.,b Masaryk Memorial Cancer Institute , Regional Centre for Applied Molecular Oncology , Žlutý kopec 7, 65653 Brno , Czech Republic
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20
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Markov OV, Mironova NL, Sennikov SV, Vlassov VV, Zenkova MA. Prophylactic Dendritic Cell-Based Vaccines Efficiently Inhibit Metastases in Murine Metastatic Melanoma. PLoS One 2015; 10:e0136911. [PMID: 26325576 PMCID: PMC4556596 DOI: 10.1371/journal.pone.0136911] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/10/2015] [Indexed: 12/16/2022] Open
Abstract
Recent data on the application of dendritic cells (DCs) as anti-tumor vaccines has shown their great potential in therapy and prophylaxis of cancer. Here we report on a comparison of two treatment schemes with DCs that display the models of prophylactic and therapeutic vaccination using three different experimental tumor models: namely, Krebs-2 adenocarcinoma (primary tumor), melanoma (B16, metastatic tumor without a primary node) and Lewis lung carcinoma (LLC, metastatic tumor with a primary node). Dendritic cells generated from bone marrow-derived DC precursors and loaded with lysate of tumor cells or transfected with the complexes of total tumor RNA with cationic liposomes were used for vaccination. Lipofectamine 2000 and liposomes consisting of helper lipid DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) and cationic lipid 2D3 (1,26-Bis(1,2-de-O-tetradecyl-rac-glycerol)-7,11,16,20-tetraazahexacosan tetrahydrocloride) were used for RNA transfection. It was shown that DCs loaded with tumor lysate were ineffective in contrast to tumor-derived RNA. Therapeutic vaccination with DCs loaded by lipoplexes RNA/Lipofectamine 2000 was the most efficient for treatment of non-metastatic Krebs-2, where a 1.9-fold tumor growth retardation was observed. Single prophylactic vaccination with DCs loaded by lipoplexes RNA/2D3 was the most efficient to treat highly aggressive metastatic tumors LLC and B16, where 4.7- and 10-fold suppression of the number of lung metastases was observed, respectively. Antimetastatic effect of single prophylactic DC vaccination in metastatic melanoma model was accompanied by the reductions in the levels of Th2-specific cytokines however the change of the levels of Th1/Th2/Th17 master regulators was not found. Failure of double prophylactic vaccination is explained by Th17-response polarization associated with autoimmune and pro-inflammatory reactions. In the case of therapeutic DC vaccine the polarization of Th1-response was found nevertheless the antimetastatic effect was less effective in comparison with prophylactic DC vaccine.
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Affiliation(s)
- Oleg V. Markov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Nadezhda L. Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey V. Sennikov
- Federal State Budgetary Institution "Research Institute of Clinical Immunology", Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Valentin V. Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
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21
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Targeted mass spectrometry for the analysis of nutritive modulation of catalase and heme oxygenase-1 expression. J Proteomics 2015; 117:58-69. [PMID: 25639505 DOI: 10.1016/j.jprot.2015.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/09/2014] [Accepted: 01/13/2015] [Indexed: 12/19/2022]
Abstract
UNLABELLED Comprehensive physiological food assessment requires recording of activity profiles. To elucidate the nutritive regulation of antioxidant enzymes, a generally applicable targeted MS method was established for the expression analysis of catalase and then adapted to heme oxygenase-1. Before tryptic digestion, target proteins were prefractionated by off-gel IEF of stimulated and control cell lysate. Targeted proteome analysis was achieved by LC coupled with scheduled selected reaction monitoring MS using 2 proteotypic peptides per protein and 3-4 transitions per peptide. Relative quantification was performed by stable isotope labeling by amino acids in cell culture (SILAC). The assay showed good correlation with results by Western blot. Linearity, precision, and sensitivity were even improved (LC/SRM vs. Western blot: 3 vs. 1 orders of magnitude, RSD 3.7-13.7% vs. 18.4%, LOD 0.2 vs. 1.6μg/mL). The developed method indicated that coffee does not modulate catalase expression in macrophages (T7cat 103±22%, T17cat 103±16%, p>0.05 vs. control), but leads to a highly significant increase of heme oxygenase-1 expression (T15Ho-1 420±24%, T22Ho-1 364±37%, p<0.001 vs. control, p>0.05 T15Ho-1 vs. T22Ho-1). In regard to multiplex options of the method, targeted proteome analysis can be a valuable tool for the comprehensive analysis of cellular effects of food components. BIOLOGICAL SIGNIFICANCE In the present study, targeted mass spectrometry was applied to determine the influence of food components on the expression of antioxidative enzymes. The results implicate that targeted proteomics may develop into a valuable tool in food science and nutrition to determine the physiological effects of nutrients. In contrast to conventional methods for expression analysis, targeted proteome analysis can be applied to monitor the effects of a food component on a broad range of cellular targets in parallel. Additionally, proteins or protein modifications can be addressed which elude immunochemical methods.
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22
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Puangpila C, Mayadunne E, El Rassi Z. Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2011-2014. Electrophoresis 2015; 36:238-52. [PMID: 25287967 PMCID: PMC4485988 DOI: 10.1002/elps.201400434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 11/07/2022]
Abstract
This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As the previous review article, the present one is concerned with proteomic sample preparation (e.g., depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article, however, is distinguished from its earlier version by expanding on capturing/enriching subphosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid-2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field.
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Affiliation(s)
- Chanida Puangpila
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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23
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Klee EW, Bondar OP, Goodmanson MK, Trushin SA, Bergstralh EJ, Singh RJ, Anderson NL, Klee GG. Serum concentrations of prostate-specific antigen measured using immune extraction, trypsin digestion, and tandem mass spectrometry quantification of LSEPAELTDAVK peptide. Arch Pathol Lab Med 2014; 138:1381-6. [PMID: 25268201 DOI: 10.5858/arpa.2013-0462-oa] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Prostate-specific antigen (PSA) is a 34-kDa glycoprotein with chymotrypsin-like enzyme activity that circulates both in free forms and complexed to various enzyme inhibitors including antichymotrypsin and α2-macroglobulin. Prostate-specific antigen bound to α2-macroglobulin is not detected by commercial PSA immunoassays. OBJECTIVE To develop a mass spectrometry assay that detects the same forms of PSA as the immunoassays, which could serve as a reference for harmonizing PSA immunoassays. DESIGN Prostate-specific antigen was immune extracted from serum, trypsin was digested, and the LSEPAELTDAVK peptide was quantitated on an API 5000 spectrometer. Calibrators were made by adding 10% free and 90% antichymotrypsin-bound PSA to female sera. The assay was standardized to the World Health Organization 96/670 reference standard. Validation of clinical utility and comparisons with 2 immunoassays (Roche cobas and Beckman Access) were performed using frozen sera aliquots from 100 men undergoing prostate biopsy (50 negative, 50 with cancer) and 5 serial samples collected over time from 5 men with advanced prostate cancer. RESULTS The antibody extraction efficiency was greater than 99%. The assay has an analytic range from 1.2 to 76 ng/mL, with precision ranging from 8.6% at 1.5 ng/mL to 5.4% at 27 ng/mL. The mass spectrometry assay correlated well with 2 immunoassays. All 3 assays showed statistically equivalent separation of prostate cancer from benign disease using receiver operating characteristic curve analysis. CONCLUSIONS This mass spectrometry assay can reliably measure PSA concentrations in human serum and could serve as a reference standard for harmonizing PSA immunoassays.
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Affiliation(s)
- Eric W Klee
- From the Departments of Health Sciences Research (Dr E. Klee and Mr Bergstralh) and Laboratory Medicine and Pathology (Drs Bondar, Trushin, Singh, and G. Klee and Ms. Goodmanson), Mayo Clinic College of Medicine, Rochester, Minnesota; and the Plasma Proteome Institute, Washington, DC (Dr Anderson)
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24
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Chen YT, Tuan LP, Chen HW, Wei IA, Chou MY, Chen HM, Tyan YC, Chen SF. Quantitative Analysis of Prostate Specific Antigen Isoforms Using Immunoprecipitation and Stable Isotope Labeling Mass Spectrometry. Anal Chem 2014; 87:545-53. [DOI: 10.1021/ac5033066] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yi-Ting Chen
- Department
of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Molecular
Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Li-Ping Tuan
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677 Taiwan
| | - Hsiao-Wei Chen
- Molecular
Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - I-An Wei
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677 Taiwan
| | - Min-Yuan Chou
- Biomedical
Technology and Devices Research Laboratories, Industrial Technology Research Institute, Chutung 31040, Taiwan
| | - Han-Min Chen
- Department
of Life Science, Catholic Fu-Jen University, Taipei 24205, Taiwan
| | - Yu-Chang Tyan
- Department
of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Sung-Fang Chen
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677 Taiwan
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25
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Wu C, Shi T, Brown JN, He J, Gao Y, Fillmore TL, Shukla AK, Moore RJ, Camp DG, Rodland KD, Qian WJ, Liu T, Smith RD. Expediting SRM assay development for large-scale targeted proteomics experiments. J Proteome Res 2014; 13:4479-87. [PMID: 25145539 PMCID: PMC4184450 DOI: 10.1021/pr500500d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Because
of its high sensitivity and specificity, selected reaction
monitoring (SRM)-based targeted proteomics has become increasingly
popular for biological and translational applications. Selection of
optimal transitions and optimization of collision energy (CE) are
important assay development steps for achieving sensitive detection
and accurate quantification; however, these steps can be labor-intensive,
especially for large-scale applications. Herein, we explored several
options for accelerating SRM assay development evaluated in the context
of a relatively large set of 215 synthetic peptide targets. We first
showed that HCD fragmentation is very similar to that of CID in triple
quadrupole (QQQ) instrumentation and that by selection of the top
6 y fragment ions from HCD spectra, >86% of the top transitions
optimized
from direct infusion with QQQ instrumentation are covered. We also
demonstrated that the CE calculated by existing prediction tools was
less accurate for 3+ precursors and that a significant increase in
intensity for transitions could be obtained using a new CE prediction
equation constructed from the present experimental data. Overall,
our study illustrated the feasibility of expediting the development
of larger numbers of high-sensitivity SRM assays through automation
of transition selection and accurate prediction of optimal CE to improve
both SRM throughput and measurement quality.
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Affiliation(s)
- Chaochao Wu
- Biological Sciences Division and ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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26
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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27
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Simon R, Passeron S, Lemoine J, Salvador A. Hydrophilic interaction liquid chromatography as second dimension in multidimensional chromatography with an anionic trapping strategy: application to prostate-specific antigen quantification. J Chromatogr A 2014; 1354:75-84. [PMID: 24931446 DOI: 10.1016/j.chroma.2014.05.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/22/2014] [Accepted: 05/24/2014] [Indexed: 12/17/2022]
Abstract
Liquid chromatography (LC) coupled with tandem mass spectrometry (MS-MS) in selected reaction monitoring mode (SRM) has become a widely used technique for the quantification of protein biomarkers in plasma and has already proven to give similar results compared to the conventional immunoassays. To improve the lack of insufficient sensitivity for quantification of low abundance protein, we propose a new two dimensional liquid chromatography (2D-LC-SRM) method for the quantitation of prostate specific antigen (PSA) in human plasma. The method centers on anion exchange cartridge between reversed-phase chromatography and hydrophilic interaction liquid chromatography (HILIC) in an on-line arrangement. The use of the anionic cartridge allows an easier online transfer of the analytes between both dimensions. Moreover, it provides an additional selectivity since the more basic peptides are not retained on this support. This setup has been applied to the quantification of prostate specific antigen (PSA) protein in plasma on a previous generation of mass spectrometer, which enabled a limit of quantification (LOQ) of 1ng/mL without any upfront immuno-depletion or intense off-line fractionation before the SRM analysis. The obtained LOQ is compatible with the required sensitivity for the clinically relevant plasma-based PSA tests.
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Affiliation(s)
- Romain Simon
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Sébastien Passeron
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Jérôme Lemoine
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Arnaud Salvador
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France.
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Fuhrman-Luck RA, Silva ML, Dong Y, Irving-Rodgers H, Stoll T, Hastie ML, Loessner D, Gorman JJ, Clements JA. Proteomic and other analyses to determine the functional consequences of deregulated kallikrein-related peptidase (KLK) expression in prostate and ovarian cancer. Proteomics Clin Appl 2014; 8:403-15. [PMID: 24535680 DOI: 10.1002/prca.201300098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/23/2013] [Accepted: 11/30/2013] [Indexed: 02/06/2023]
Abstract
Rapidly developing proteomic tools are improving detection of deregulated kallikrein-related peptidase (KLK) expression, at the protein level, in prostate and ovarian cancer, as well as facilitating the determination of functional consequences downstream. MS-driven proteomics uniquely allows for the detection, identification, and quantification of thousands of proteins in a complex protein pool, and this has served to identify certain KLKs as biomarkers for these diseases. In this review, we describe applications of this technology in KLK biomarker discovery and elucidate MS-based techniques that have been used for unbiased, global screening of KLK substrates within complex protein pools. Although MS-based KLK degradomic studies are limited to date, they helped to discover an array of novel KLK substrates. Substrates identified by MS-based degradomics are reported with improved confidence over those determined by incubating a purified or recombinant substrate and protease of interest, in vitro. We propose that these novel proteomic approaches represent the way forward for KLK research, in order to correlate proteolysis of biological substrates with tissue-related consequences, toward clinical targeting of KLK expression and function for cancer diagnosis, prognosis, and therapies.
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Affiliation(s)
- Ruth Anna Fuhrman-Luck
- Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Brisbane, Australia; Australian Prostate Cancer Research Centre - Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, Australia
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29
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Schutzer SE. Rapidly maturing field of proteomics: a gateway to studying diseases. Proteomics 2014; 14:991-3. [PMID: 24668871 DOI: 10.1002/pmic.201400091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 03/21/2014] [Indexed: 11/11/2022]
Abstract
The proteomics work reported by Smith et al. represents a giant step forward in characterizing the cerebrospinal fluid (CSF) proteome in mouse models of human diseases. Whereas prior studies were limited to analysis of CSF pools, Smith et al. (Proteomics 2014, 14, 1102-1106) base their conclusions on data derived from individual mice, thereby capturing a fuller range of the biological diversity present. These results underscore how far proteomics has come in the past few years, developing into a modern tool with the capacity to remove bottlenecks in the study of neuropsychiatric diseases. Past efforts with mass spectrometry (MS) have been hampered by limitations in access to CSF samples, and small volumes when available. These barriers have been overcome with newer MS platforms and advances in sample preparation. We are far closer than before to producing the production of clinically useful proteomic data for biomarker discovery and for deriving insights into pathogenesis that can lead to more effective treatments for many diseases.
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Affiliation(s)
- Steven E Schutzer
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
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30
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Chambers AG, Percy AJ, Simon R, Borchers CH. MRM for the verification of cancer biomarker proteins: recent applications to human plasma and serum. Expert Rev Proteomics 2014; 11:137-48. [PMID: 24476379 DOI: 10.1586/14789450.2014.877346] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Accurate cancer biomarkers are needed for early detection, disease classification, prediction of therapeutic response and monitoring treatment. While there appears to be no shortage of candidate biomarker proteins, a major bottleneck in the biomarker pipeline continues to be their verification by enzyme linked immunosorbent assays. Multiple reaction monitoring (MRM), also known as selected reaction monitoring, is a targeted mass spectrometry approach to protein quantitation and is emerging to bridge the gap between biomarker discovery and clinical validation. Highly multiplexed MRM assays are readily configured and enable simultaneous verification of large numbers of candidates facilitating the development of biomarker panels which can increase specificity. This review focuses on recent applications of MRM to the analysis of plasma and serum from cancer patients for biomarker verification. The current status of this approach is discussed along with future directions for targeted mass spectrometry in clinical biomarker validation.
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Affiliation(s)
- Andrew G Chambers
- University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham St, Victoria, BC V8Z 7X8, Canada
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31
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Percy AJ, Byrns S, Chambers AG, Borchers CH. Targeted quantitation of CVD-linked plasma proteins for biomarker verification and validation. Expert Rev Proteomics 2014; 10:567-78. [DOI: 10.1586/14789450.2013.856763] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Shi T, Gao Y, Quek SI, Fillmore TL, Nicora CD, Su D, Zhao R, Kagan J, Srivastava S, Rodland KD, Liu T, Smith RD, Chan DW, Camp DG, Liu AY, Qian WJ. A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum. J Proteome Res 2013; 13:875-82. [PMID: 24251762 DOI: 10.1021/pr400912c] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Anterior gradient 2 (AGR2) is a secreted, cancer-associated protein in many types of epithelial cancer cells. We developed a highly sensitive targeted mass spectrometric assay for quantification of AGR2 in urine and serum. Digested peptides from clinical samples were processed by PRISM (high pressure and high resolution separations coupled with intelligent selection and multiplexing), which incorporates high pH reversed-phase liquid chromatography (LC) separations to fractionate and select target fractions for follow-on LC-selected reaction monitoring (LC-SRM) analyses. The PRISM-SRM assay for AGR2 showed a reproducibility of <10% CV and limit of quantification (LOQ) values of ∼130 pg/mL in serum and ∼10 pg per 100 μg of total protein mass in urine, respectively. A good correlation (R(2) = 0.91) was observed for the measurable AGR2 concentrations in urine between SRM and enzyme-linked immunosorbent assay (ELISA). On the basis of an initial cohort of 37 subjects, urinary AGR2/PSA concentration ratios showed a significant difference (P = 0.026) between noncancer and cancer. Large clinical cohort studies are needed for the validation of AGR2 as a useful diagnostic biomarker for prostate cancer. Our work validated the approach of identifying candidate secreted protein biomarkers through genomics and measurement by targeted proteomics, especially for proteins where no immunoassays are available.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352
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33
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Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 2013; 5:2837-56. [DOI: 10.4155/bio.13.245] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Quantitative plasma proteomics, through the use of targeted MRM-MS and isotopically labeled standards, is emerging as a popular technique to address biological- and biomedical-centered queries. High precision and accuracy are essential in such measurements, particularly in protein biomarker research where translation to the clinic is sought. Standardized procedures and routine performance evaluation of all stages of the workflow (both pre-analytical and analytical) are therefore imperative to satisfy these requisites and enable high inter-laboratory reproducibility and transferability. In this review, we first discuss the pre-analytical and analytical variables that can affect the precision and accuracy of ‘absolute’ quantitative plasma proteomic measurements. Proposed strategies to limit such variability will then be highlighted and unmet needs for future exploration will be noted. Although there is no way to conduct a truly comprehensive review on this broad, rapidly changing topic, we have highlighted key aspects and included references to review articles on various sub-topics.
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34
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Végvári Á, Sjödin K, Rezeli M, Malm J, Lilja H, Laurell T, Marko-Varga G. Identification of a novel proteoform of prostate specific antigen (SNP-L132I) in clinical samples by multiple reaction monitoring. Mol Cell Proteomics 2013; 12:2761-73. [PMID: 23842001 PMCID: PMC3790289 DOI: 10.1074/mcp.m113.028365] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/07/2013] [Indexed: 12/12/2022] Open
Abstract
Prostate specific antigen (PSA) is a well-established tumor marker that is frequently employed as model biomarker in the development and evaluation of emerging quantitative proteomics techniques, partially as a result of wide access to commercialized immunoassays serving as "gold standards." We designed a multiple reaction monitoring (MRM) assay to detect PSA proteoforms in clinical samples (n = 72), utilizing the specificity and sensitivity of the method. We report, for the first time, a PSA proteoform coded by SNP-L132I (rs2003783) that was observed in nine samples in both heterozygous (n = 7) and homozygous (n = 2) expression profiles. Other isoforms of PSA, derived from protein databases, were not identified by four unique proteotypic tryptic peptides. We have also utilized our MRM assay for precise quantitative analysis of PSA concentrations in both seminal and blood plasma samples. The analytical performance was evaluated, and close agreement was noted between quantitations based on three selected peptides (LSEPAELTDAVK, IVGGWECEK, and SVILLGR) and a routinely used commercialized immunoassay. Additionally, we disclose that the peptide IVGGWECEK is shared with kallikrein-related peptidase 2 and therefore is not unique for PSA. Thus, we propose the use of another tryptic sequence (SVILLGR) for accurate MRM quantification of PSA in clinical samples.
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Affiliation(s)
- Ákos Végvári
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Karin Sjödin
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Melinda Rezeli
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Johan Malm
- ¶Dept. of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, SE-205 02 Malmö, Sweden
| | - Hans Lilja
- ¶Dept. of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, SE-205 02 Malmö, Sweden
- ‖Depts. of Laboratory Medicine, Surgery (Urology), and Medicine (GU-Oncology), Memorial Sloan-Kettering Cancer Center, New York, New York 10065
- **Nuffield Dept. of Surgical Sciences, University of Oxford, Oxford, OX3 9DU UK
- ‡‡Institute of Biomedical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland
| | - Thomas Laurell
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- §§Dept. of Biomedical Engineering, Dongguk University, Seoul, 100-715, South Korea
| | - György Marko-Varga
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- ¶¶First Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, 160-0023 Japan
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Shi T, Fillmore TL, Gao Y, Zhao R, He J, Schepmoes AA, Nicora CD, Wu C, Chambers JL, Moore RJ, Kagan J, Srivastava S, Liu AY, Rodland KD, Liu T, Camp DG, Smith RD, Qian WJ. Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis. Anal Chem 2013; 85:9196-203. [PMID: 24004026 DOI: 10.1021/ac402105s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Long-gradient separations coupled to tandem mass spectrometry (MS) were recently demonstrated to provide a deep proteome coverage for global proteomics; however, such long-gradient separations have not been explored for targeted proteomics. Herein, we investigate the potential performance of the long-gradient separations coupled with selected reaction monitoring (LG-SRM) for targeted protein quantification. Direct comparison of LG-SRM (5 h gradient) and conventional liquid chromatography (LC)-SRM (45 min gradient) showed that the long-gradient separations significantly reduced background interference levels and provided an 8- to 100-fold improvement in limit of quantification (LOQ) for target proteins in human female serum. On the basis of at least one surrogate peptide per protein, an LOQ of 10 ng/mL was achieved for the two spiked proteins in nondepleted human serum. The LG-SRM detection of seven out of eight endogenous plasma proteins expressed at ng/mL or subng/mL levels in clinical patient sera was also demonstrated. A correlation coefficient of >0.99 was observed for the results of LG-SRM and enzyme-linked immunosorbent assay (ELISA) measurements for prostate-specific antigen (PSA) in selected patient sera. Further enhancement of LG-SRM sensitivity was achieved by applying front-end IgY14 immunoaffinity depletion. Besides improved sensitivity, LG-SRM potentially offers much higher multiplexing capacity than conventional LC-SRM due to an increase in average peak widths (~3-fold) for a 300 min gradient compared to a 45 min gradient. Therefore, LG-SRM holds great potential for bridging the gap between global and targeted proteomics due to its advantages in both sensitivity and multiplexing capacity.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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36
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Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:917-26. [PMID: 23806606 DOI: 10.1016/j.bbapap.2013.06.008] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/27/2013] [Accepted: 06/14/2013] [Indexed: 11/23/2022]
Abstract
Accurate and rapid protein quantitation is essential for screening biomarkers for disease stratification and monitoring, and to validate the hundreds of putative markers in human biofluids, including blood plasma. An analytical method that utilizes stable isotope-labeled standard (SIS) peptides and selected/multiple reaction monitoring-mass spectrometry (SRM/MRM-MS) has emerged as a promising technique for determining protein concentrations. This targeted approach has analytical merit, but its true potential (in terms of sensitivity and multiplexing) has yet to be realized. Described herein is a method that extends the multiplexing ability of the MRM method to enable the quantitation 142 high-to-moderate abundance proteins (from 31mg/mL to 44ng/mL) in undepleted and non-enriched human plasma in a single run. The proteins have been reported to be associated to a wide variety of non-communicable diseases (NCDs), from cardiovascular disease (CVD) to diabetes. The concentrations of these proteins in human plasma are inferred from interference-free peptides functioning as molecular surrogates (2 peptides per protein, on average). A revised data analysis strategy, involving the linear regression equation of normal control plasma, has been instituted to enable the facile application to patient samples, as demonstrated in separate nutrigenomics and CVD studies. The exceptional robustness of the LC/MS platform and the quantitative method, as well as its high throughput, makes the assay suitable for application to patient samples for the verification of a condensed or complete protein panel. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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37
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Shi T, Sun X, Gao Y, Fillmore TL, Schepmoes AA, Zhao R, He J, Moore RJ, Kagan J, Rodland KD, Liu T, Liu AY, Smith RD, Tang K, Camp DG, Qian WJ. Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion. J Proteome Res 2013; 12:3353-61. [PMID: 23763644 DOI: 10.1021/pr400178v] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We recently reported an antibody-free targeted protein quantification strategy, termed high-pressure, high-resolution separations with intelligent selection and multiplexing (PRISM), for achieving significantly enhanced sensitivity using selected reaction monitoring (SRM) mass spectrometry. Integrating PRISM with front-end IgY14 immunoaffinity depletion, sensitive detection of targeted proteins at 50-100 pg/mL levels in human blood plasma/serum was demonstrated. However, immunoaffinity depletion is often associated with undesired losses of target proteins of interest. Herein we report further evaluation of PRISM-SRM quantification of low-abundance serum proteins without immunoaffinity depletion. Limits of quantification (LOQ) at low ng/mL levels with a median coefficient of variation (CV) of ∼12% were achieved for proteins spiked into human female serum. PRISM-SRM provided >100-fold improvement in the LOQ when compared to conventional LC-SRM measurements. PRISM-SRM was then applied to measure several low-abundance endogenous serum proteins, including prostate-specific antigen (PSA), in clinical prostate cancer patient sera. PRISM-SRM enabled confident detection of all target endogenous serum proteins except the low pg/mL-level cardiac troponin T. A correlation coefficient >0.99 was observed for PSA between the results from PRISM-SRM and immunoassays. Our results demonstrate that PRISM-SRM can successfully quantify low ng/mL proteins in human plasma or serum without depletion. We anticipate broad applications for PRISM-SRM quantification of low-abundance proteins in candidate biomarker verification and systems biology studies.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
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Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum. Proc Natl Acad Sci U S A 2012; 109:15395-400. [PMID: 22949669 DOI: 10.1073/pnas.1204366109] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sensitive detection of low-abundance proteins in complex biological samples has typically been achieved by immunoassays that use antibodies specific to target proteins; however, de novo development of antibodies is associated with high costs, long development lead times, and high failure rates. To address these challenges, we developed an antibody-free strategy that involves PRISM (high-pressure, high-resolution separations coupled with intelligent selection and multiplexing) for sensitive selected reaction monitoring (SRM)-based targeted protein quantification. The strategy capitalizes on high-resolution reversed-phase liquid chromatographic separations for analyte enrichment, intelligent selection of target fractions via on-line SRM monitoring of internal standards, and fraction multiplexing before nano-liquid chromatography-SRM quantification. Application of this strategy to human plasma/serum demonstrated accurate and reproducible quantification of proteins at concentrations in the 50-100 pg/mL range, which represents a major advance in the sensitivity of targeted protein quantification without the need for specific-affinity reagents. Application to a set of clinical serum samples illustrated an excellent correlation between the results obtained from the PRISM-SRM assay and those from clinical immunoassay for the prostate-specific antigen level.
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40
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Angel TE, Jacobs JM, Smith RP, Pasternack MS, Elias S, Gritsenko MA, Shukla A, Gilmore EC, McCarthy C, Camp DG, Smith RD, Warren HS. Cerebrospinal fluid proteome of patients with acute Lyme disease. J Proteome Res 2012; 11:4814-22. [PMID: 22900834 DOI: 10.1021/pr300577p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
During acute Lyme disease, bacteria can disseminate to the central nervous system (CNS), leading to the development of meningitis and other neurologic symptoms. Here we have analyzed pooled cerebrospinal fluid (CSF) allowing a deep view into the proteome for patients diagnosed with early disseminated Lyme disease and CSF inflammation. Additionally, we analyzed individual patient samples and quantified differences in protein abundance employing label-free quantitative mass spectrometry-based methods. We identified 108 proteins that differ significantly in abundance in patients with acute Lyme disease from controls. Comparison between infected patients and control subjects revealed differences in proteins in the CSF associated with cell death localized to brain synapses and others that likely originate from brain parenchyma.
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Affiliation(s)
- Thomas E Angel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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