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Song JG, Baral KC, Kim GL, Park JW, Seo SH, Kim DH, Jung DH, Ifekpolugo NL, Han HK. Quantitative analysis of therapeutic proteins in biological fluids: recent advancement in analytical techniques. Drug Deliv 2023; 30:2183816. [PMID: 36880122 PMCID: PMC10003146 DOI: 10.1080/10717544.2023.2183816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Pharmaceutical application of therapeutic proteins has been continuously expanded for the treatment of various diseases. Efficient and reliable bioanalytical methods are essential to expedite the identification and successful clinical development of therapeutic proteins. In particular, selective quantitative assays in a high-throughput format are critical for the pharmacokinetic and pharmacodynamic evaluation of protein drugs and to meet the regulatory requirements for new drug approval. However, the inherent complexity of proteins and many interfering substances presented in biological matrices have a great impact on the specificity, sensitivity, accuracy, and robustness of analytical assays, thereby hindering the quantification of proteins. To overcome these issues, various protein assays and sample preparation methods are currently available in a medium- or high-throughput format. While there is no standard or universal approach suitable for all circumstances, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay often becomes a method of choice for the identification and quantitative analysis of therapeutic proteins in complex biological samples, owing to its high sensitivity, specificity, and throughput. Accordingly, its application as an essential analytical tool is continuously expanded in pharmaceutical R&D processes. Proper sample preparation is also important since clean samples can minimize the interference from co-existing substances and improve the specificity and sensitivity of LC-MS/MS assays. A combination of different methods can be utilized to improve bioanalytical performance and ensure more accurate quantification. This review provides an overview of various protein assays and sample preparation methods, with particular emphasis on quantitative protein analysis by LC-MS/MS.
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Affiliation(s)
- Jae Geun Song
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Kshitis Chandra Baral
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Gyu-Lin Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Ji-Won Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Soo-Hwa Seo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Da-Hyun Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Dong Hoon Jung
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Nonye Linda Ifekpolugo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Hyo-Kyung Han
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
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Meng J, Zhang Y, Wang G, Ji M, Wang B, He G, Wang Q, Bai F, Xu K, Yuan D, Li S, Cheng Y, Wei S, Fu C, Wang G, Zhou G. Conduction of a chemical structure-guided metabolic phenotype analysis method targeting phenylpropane pathway via LC-MS: Ginkgo biloba and soybean as examples. Food Chem 2022; 390:133155. [PMID: 35576806 DOI: 10.1016/j.foodchem.2022.133155] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 11/04/2022]
Abstract
The phenylpropane pathway (PPP) is one of the most extensively investigated metabolic routes. This pathway biosynthesizes many important active ingredients such as phenylpropanoids and flavonoids that affect the flavor, taste and nutrients of food. How to elucidate the metabolic phenotype of PPP is fundamental in food research and development. In this study, we designed a structural periodical table filled with 103 metabolites produced from PPP. All of them especially the 62 structural isomers were qualified and quantified with high resolution and sensitivity via multiple reaction mode in liquid chromatography tandem triple quadrupole mass spectrometry. Ginkgo biloba and soybean were used as samples for the practical application of this method: The delicate spatial-temporal metabolic balance of PPP from ginkgo biloba has been first elucidated; It is first confirmed that the salt and draught stresses could redirect the biosynthesis trend of PPP to produce more isoflavones in soybean leaves.
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Affiliation(s)
- Jie Meng
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Yiran Zhang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Guolin Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Meijing Ji
- College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Bo Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Guo He
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Qianwen Wang
- Central Public Laboratory of Qingdao Agricultural University, Qingdao 266109, China
| | - Fali Bai
- Public Laboratory of Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Kun Xu
- Central Public Laboratory of Qingdao Agricultural University, Qingdao 266109, China
| | - Dongliang Yuan
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuai Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Yue Cheng
- College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuhui Wei
- College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Gongke Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China.
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Schleicher K, Hester S, Stegmann M, Zaccolo M. Quantitative Phosphoproteomics to Study cAMP Signaling. Methods Mol Biol 2022; 2483:281-296. [PMID: 35286683 DOI: 10.1007/978-1-0716-2245-2_18] [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: 11/26/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) signaling activates multiple downstream cellular targets in response to different stimuli. Specific phosphorylation of key target proteins via activation of the cAMP effector protein kinase A (PKA) is achieved via signal compartmentalization. Termination of the cAMP signal is mediated by phosphodiesterases (PDEs), a diverse group of enzymes comprising several families that localize to distinct cellular compartments. By studying the effects of inhibiting individual PDE families on the phosphorylation of specific targets it is possible to gain information on the subcellular spatial organization of this signaling pathway.We describe a phosphoproteomic approach that can detect PDE family-specific phosphorylation changes in cardiac myocytes against a high phosphorylation background. The method combines dimethyl labeling and titanium dioxide-mediated phosphopeptide enrichment, followed by tandem mass spectrometry.
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Affiliation(s)
- Katharina Schleicher
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
| | - Svenja Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Monika Stegmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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Casein kinase TbCK1.2 regulates division of kinetoplast DNA, and movement of basal bodies in the African trypanosome. PLoS One 2021; 16:e0249908. [PMID: 33861760 PMCID: PMC8051774 DOI: 10.1371/journal.pone.0249908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/26/2021] [Indexed: 01/15/2023] Open
Abstract
The single mitochondrial nucleoid (kinetoplast) of Trypanosoma brucei is found proximal to a basal body (mature (mBB)/probasal body (pBB) pair). Kinetoplast inheritance requires synthesis of, and scission of kinetoplast DNA (kDNA) generating two kinetoplasts that segregate with basal bodies into daughter cells. Molecular details of kinetoplast scission and the extent to which basal body separation influences the process are unavailable. To address this topic, we followed basal body movements in bloodstream trypanosomes following depletion of protein kinase TbCK1.2 which promotes kinetoplast division. In control cells we found that pBBs are positioned 0.4 um from mBBs in G1, and they mature after separating from mBBs by at least 0.8 um: mBB separation reaches ~2.2 um. These data indicate that current models of basal body biogenesis in which pBBs mature in close proximity to mBBs may need to be revisited. Knockdown of TbCK1.2 produced trypanosomes containing one kinetoplast and two nuclei (1K2N), increased the percentage of cells with uncleaved kDNA 400%, decreased mBB spacing by 15%, and inhibited cytokinesis 300%. We conclude that (a) separation of mBBs beyond a threshold of 1.8 um correlates with division of kDNA, and (b) TbCK1.2 regulates kDNA scission. We propose a Kinetoplast Division Factor hypothesis that integrates these data into a pathway for biogenesis of two daughter mitochondrial nucleoids.
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Flowers SA, Lane CS, Karlsson NG. Deciphering Isomers with a Multiple Reaction Monitoring Method for the Complete Detectable O-Glycan Repertoire of the Candidate Therapeutic, Lubricin. Anal Chem 2019; 91:9819-9827. [PMID: 31246420 DOI: 10.1021/acs.analchem.9b01485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosylation is a fundamental post-translational modification, occurring on half of all proteins. Despite its significance, our understanding is limited, in part due to the inherent difficulty in studying these branched, multi-isomer structures. Accessible, detailed, and quantifiable methods for studying glycans, particularly O-glycans, are needed. Here we take a multiple reaction monitoring (MRM) approach to differentiate and relatively quantify all detectable glycans, including isomers, on the heavily O-glycosylated protein lubricin. Lubricin (proteoglycan 4) is essential for lubrication of the joint and eye. Given the therapeutic potential of lubricin, it is essential to understand its O-glycan repertoire in biological and recombinantly produced samples. O-Glycans were released by reductive β-elimination and defined, showing a range of 26 neutral, sulfated, sialylated, and both sulfated and sialylated core 1 (Galβ1-3GalNAcα1-) and core 2 (Galβ1-3(GlcNAcβ1-6)GalNAcα1-) structures. Isomer-specific MRM transitions allowed effective differentiation of neutral glycan isomers as well as sulfated isomeric structures, where the sulfate was retained on the fragment ions. This strategy was not as effective with labile sialylated structures; instead, it was observed that the optimal collision energy for the m/z 290.1 sialic acid B-fragment differed consistently between sialic acid isomers, allowing differentiation between isomers when fragmentation spectra were insufficient. This approach was also effective for purchased Neu5Acα2-3Galβ1-4Glc and Neu5Acα2-6Galβ1-4Glc and for Neu5Acα2-3Galβ1-4GlcNAc and Neu5Acα2-6Galβ1-4GlcNAc linkage isomers with the Neu5Acα2-6 consistently requiring more energy for optimal generation of the m/z 290.1 fragment. Overall, this method provides an effective and easily accessible approach for the quantification and annotation of complex released O-glycan samples.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden.,Department of Neuroscience , Georgetown University , 3970 Reservoir Road NW, New Research Building EP20 , Washington, D.C. , United States
| | - Catherine S Lane
- SCIEX , Phoenix House, Lakeside Drive, Centre Park , Warrington WA1 1RX , United Kingdom
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden
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Identification of Protein Phosphorylation Sites by Advanced LC-ESI-MS/MS Methods. Methods Mol Biol 2019. [PMID: 31256379 DOI: 10.1007/978-1-4939-9055-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Phosphorylation, the process by which a phosphate group is attached to a preexisting protein, is an evolutionarily and metabolically cheap way to change the protein's surface and properties. It is presumably for that reason that it is the most widespread protein modification: An estimated 10-30% of all proteins are subject to phosphorylation.MS-based methods are the methods of choice for the identification of phosphorylation sites; however biochemical pre-fractionation and enrichment protocols will be needed to produce suitable samples in the case of low-stoichiometry phosphorylation. Using emerging MS-based technology, the elucidation of the "phosphoproteome," a comprehensive inventory of phosphorylation sites, will become a realistic goal. However, validating these findings in a cellular context and defining their biological meaning remains a daunting task, which will inevitably require extensive and time-consuming additional biological research.
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Gupta MB, Abu Shehab M, Nygard K, Biggar K, Singal SS, Santoro N, Powell TL, Jansson T. IUGR Is Associated With Marked Hyperphosphorylation of Decidual and Maternal Plasma IGFBP-1. J Clin Endocrinol Metab 2019; 104:408-422. [PMID: 30124960 PMCID: PMC6306389 DOI: 10.1210/jc.2018-00820] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 08/13/2018] [Indexed: 01/03/2023]
Abstract
CONTEXT The mechanisms underpinning intrauterine growth restriction (IUGR), as a result of placental insufficiency, remain poorly understood, no specific treatment is available, and clinically useful biomarkers for early detection are lacking. OBJECTIVE We hypothesized that human IUGR is associated with inhibition of mechanistic target of rapamycin (mTOR) and activation of amino acid response (AAR) signaling, increased protein kinase casein kinase-2 (CK2) activity, and increased insulin-like growth factor-binding protein 1 (IGFBP-1) expression and phosphorylation in decidua and that maternal plasma IGFBP-1 hyperphosphorylation in the first trimester predicts later development of IUGR. DESIGN, SETTING, AND PARTICIPANTS Decidua [n = 16 appropriate-for-gestational age (AGA); n = 16 IUGR] and maternal plasma (n = 13 AGA; n = 13 IUGR) were collected at delivery from two different cohorts. In addition, maternal plasma was obtained in the late first trimester from a third cohort of women (n = 7) who later delivered an AGA or IUGR infant. MAIN OUTCOME MEASURES Total IGFBP-1 expression and phosphorylation (Ser101/Ser119/Ser169), mTOR, AAR, and CK2 activity in decidua and IGFBP-1 concentration and phosphorylation in maternal plasma. RESULTS We show that decidual IGFBP-1 expression and phosphorylation are increased, mTOR is markedly inhibited, and AAR and CK2 are activated in IUGR. Moreover, IGFBP-1 hyperphosphorylation in first-trimester maternal plasma is associated with the development of IUGR. CONCLUSIONS These data are consistent with the possibility that the decidua functions as a nutrient sensor linking limited oxygen and nutrient availability to increased IGFBP-1 phosphorylation, possibly mediated by mTOR and AAR signaling. IGFBP-1 hyperphosphorylation in first-trimester maternal plasma may serve as a predictive IUGR biomarker, allowing early intervention.
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Affiliation(s)
- Madhulika B Gupta
- Department of Pediatrics, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Correspondence and Reprint Requests: Madhulika B. Gupta, PhD, Children’s Health Research Institute, VRL Room A5-136 (WC), 800 Commissioners Road E., London, Ontario N6C 2VD, Canada. E-mail:
| | - Majida Abu Shehab
- Department of Pediatrics, University of Western Ontario, London, Ontario, Canada
| | - Karen Nygard
- Biotron Laboratory, University of Western Ontario, London, Ontario, Canada
| | - Kyle Biggar
- Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Sahil S Singal
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Nanette Santoro
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Theresa L Powell
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Thomas Jansson
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Wu X, Xing X, Dowlut D, Zeng Y, Liu J, Liu X. Integrating phosphoproteomics into kinase-targeted cancer therapies in precision medicine. J Proteomics 2019; 191:68-79. [DOI: 10.1016/j.jprot.2018.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/20/2018] [Accepted: 03/31/2018] [Indexed: 12/12/2022]
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Woods AG, Sokolowska I, Ngounou Wetie AG, Channaveerappa D, Dupree EJ, Jayathirtha M, Aslebagh R, Wormwood KL, Darie CC. Mass Spectrometry for Proteomics-Based Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:1-26. [DOI: 10.1007/978-3-030-15950-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Jiang H, Zhang L, Zhang Y, Xie L, Wang Y, Lu H. HST-MRM-MS: A Novel High-Sample-Throughput Multiple Reaction Monitoring Mass Spectrometric Method for Multiplex Absolute Quantitation of Hepatocellular Carcinoma Serum Biomarker. J Proteome Res 2018; 18:469-477. [PMID: 30346787 DOI: 10.1021/acs.jproteome.8b00790] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Absolute quantification of clinical biomarkers by mass spectrometry (MS) has been challenged due to low sample-throughput of current multiple reaction monitoring (MRM) methods. For this problem to be overcome, in this work, a novel high-sample-throughput multiple reaction monitoring mass spectrometric (HST-MRM-MS) quantification approach is developed to achieve simultaneous quantification of 24 samples. Briefly, triplex dimethyl reagents (L, M, and H) and eight-plex iTRAQ reagents were used to label the N- and C-termini of the Lys C-digested peptides, respectively. The triplex dimethyl labeling produces three coelute peaks in MRM traces, and the iTRAQ labeling produces eight peaks in MS2, resulting in 24 (3×8) channels in a single experiment. HST-MRM-MS has shown good accuracy ( R2 > 0.98 for absolute quantification), reproducibility (RSD < 15%), and linearity (2-3 orders of magnitude). Moreover, the novel method has been successfully applied in quantifying serum biomarkers in hepatocellular carcinoma (HCC)-related serum samples. In conclusion, HST-MRM-MS is an accurate, high-sample-throughput, and broadly applicable MS-based absolute quantification method.
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Paredes R, Schneider M, Stevens A, White DJ, Williamson AJK, Muter J, Pearson S, Kelly JR, Connors K, Wiseman DH, Chadwick JA, Löffler H, Teng HY, Lovell S, Unwin R, van de Vrugt HJ, Smith H, Kustikova O, Schambach A, Somervaille TCP, Pierce A, Whetton AD, Meyer S. EVI1 carboxy-terminal phosphorylation is ATM-mediated and sustains transcriptional modulation and self-renewal via enhanced CtBP1 association. Nucleic Acids Res 2018; 46:7662-7674. [PMID: 29939287 PMCID: PMC6125627 DOI: 10.1093/nar/gky536] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 01/15/2023] Open
Abstract
The transcriptional regulator EVI1 has an essential role in early hematopoiesis and development. However, aberrantly high expression of EVI1 has potent oncogenic properties and confers poor prognosis and chemo-resistance in leukemia and solid tumors. To investigate to what extent EVI1 function might be regulated by post-translational modifications we carried out mass spectrometry- and antibody-based analyses and uncovered an ATM-mediated double phosphorylation of EVI1 at the carboxy-terminal S858/S860 SQS motif. In the presence of genotoxic stress EVI1-WT (SQS), but not site mutated EVI1-AQA was able to maintain transcriptional patterns and transformation potency, while under standard conditions carboxy-terminal mutation had no effect. Maintenance of hematopoietic progenitor cell clonogenic potential was profoundly impaired with EVI1-AQA compared with EVI1-WT, in particular in the presence of genotoxic stress. Exploring mechanistic events underlying these observations, we showed that after genotoxic stress EVI1-WT, but not EVI1-AQA increased its level of association with its functionally essential interaction partner CtBP1, implying a role for ATM in regulating EVI1 protein interactions via phosphorylation. This aspect of EVI1 regulation is therapeutically relevant, as chemotherapy-induced genotoxicity might detrimentally sustain EVI1 function via stress response mediated phosphorylation, and ATM-inhibition might be of specific targeted benefit in EVI1-overexpressing malignancies.
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Affiliation(s)
- Roberto Paredes
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Marion Schneider
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Adam Stevens
- Manchester Academic Health Science Centre, Manchester, UK
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health M13 9WL, University of Manchester, UK
| | - Daniel J White
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew J K Williamson
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Joanne Muter
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Stella Pearson
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - James R Kelly
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Kathleen Connors
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Daniel H Wiseman
- Manchester Academic Health Science Centre, Manchester, UK
- Leukaemia Biology Group, CRUK Manchester Institute, Manchester M20 4XB, UK
| | - John A Chadwick
- Manchester Academic Health Science Centre, Manchester, UK
- Leukaemia Biology Group, CRUK Manchester Institute, Manchester M20 4XB, UK
| | - Harald Löffler
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Hsiang Ying Teng
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Simon Lovell
- Manchester Academic Health Science Centre, Manchester, UK
- Evolution, Systems and Genomics Domain,Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard Unwin
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Henri J van de Vrugt
- Oncogenetics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Helen Smith
- Manchester Academic Health Science Centre, Manchester, UK
- Evolution, Systems and Genomics Domain,Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Olga Kustikova
- Institute of Experimental Hematology, Hannover Medical School; Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School; Hannover, Germany
| | - Tim C P Somervaille
- Manchester Academic Health Science Centre, Manchester, UK
- Leukaemia Biology Group, CRUK Manchester Institute, Manchester M20 4XB, UK
| | - Andrew Pierce
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Anthony D Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester M13 9NQ, UK
| | - Stefan Meyer
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Palatine Road, Manchester M20 3LI, UK
- Manchester Academic Health Science Centre, Manchester, UK
- Department of Paediatric Haematology and Oncology, Royal Manchester Children's Hospital, Manchester M13 9WL, UK
- Young Oncology Unit, The Christie NHS Foundation Trust, Manchester M20 4XB, UK
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Tsai CH, Chen YT, Chang YH, Hsueh C, Liu CY, Chang YS, Chen CL, Yu JS. Systematic verification of bladder cancer-associated tissue protein biomarker candidates in clinical urine specimens. Oncotarget 2018; 9:30731-30747. [PMID: 30112103 PMCID: PMC6089400 DOI: 10.18632/oncotarget.24578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 02/20/2018] [Indexed: 12/29/2022] Open
Abstract
Bladder cancer biomarkers currently approved by the Food and Drug Administration are insufficiently reliable for use in non-invasive clinical diagnosis. Verification/validation of numerous biomarker candidates for BC detection is a crucial bottleneck for novel biomarker development. A multiplexed liquid chromatography multiple-reaction-monitoring mass spectrometry assay of 122 proteins, including 118 up-regulated tissue proteins, two known bladder cancer biomarkers and two housekeeping gene products, was successfully established for protein quantification in clinical urine specimens. Quantification of 122 proteins was performed on a large cohort of urine specimens representing a variety of conditions, including 142 hernia, 126 bladder cancer, 67 hematuria, and 59 urinary tract infection samples. ANXA3 (annexin A3) and HSPE1 (heat shock protein family E member 1), which showed the highest detection frequency in bladder cancer samples, were selected for further validation. Western blotting showed that urinary ANXA3 and HSPE1 protein levels were higher in bladder cancer samples than in hernia samples, and enzyme-linked immunosorbent assays confirmed a higher urinary concentration of HSPE1 in bladder cancer than in hernia, hematuria and urinary tract infection. Immunohistochemical analyses showed significantly elevated levels of HSPE1 in tumor cells compared with non-cancerous bladder epithelial cells, suggesting that HSPE1 could be a useful tumor tissue marker for the specific detection of bladder cancer. Collectively, our findings provide valuable information for future validation of potential biomarkers for bladder cancer diagnosis.
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Affiliation(s)
- Cheng-Han Tsai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Ying-Hsu Chang
- Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chuen Hsueh
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Pathology, Chang Gung Memorial Hospital, Linkou, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Chung-Yi Liu
- Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chien-Lun Chen
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.,Research Center for Food and Cosmetic Safety, Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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13
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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14
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Borràs E, Sabidó E. What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry. Proteomics 2017; 17. [PMID: 28719092 DOI: 10.1002/pmic.201700180] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 12/14/2022]
Abstract
Targeted proteomics has gained significant popularity in mass spectrometry-based protein quantification as a method to detect proteins of interest with high sensitivity, quantitative accuracy and reproducibility. However, with the emergence of a wide variety of targeted proteomics methods, some of them with high-throughput capabilities, it is easy to overlook the essence of each method and to determine what makes each of them a targeted proteomics method. In this viewpoint, we revisit the main targeted proteomics methods and classify them in four categories differentiating those methods that perform targeted data acquisition from targeted data analysis, and those methods that are based on peptide ion data (MS1 targeted methods) from those that rely on the peptide fragments (MS2 targeted methods).
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Affiliation(s)
- Eva Borràs
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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15
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Chan KY, Alonso-Nuñez M, Grallert A, Tanaka K, Connolly Y, Smith DL, Hagan IM. Dialogue between centrosomal entrance and exit scaffold pathways regulates mitotic commitment. J Cell Biol 2017; 216:2795-2812. [PMID: 28774892 PMCID: PMC5584178 DOI: 10.1083/jcb.201702172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 11/22/2022] Open
Abstract
The fission yeast scaffold molecule Sid4 anchors the septum initiation network to the spindle pole body (SPB, centrosome equivalent) to control mitotic exit events. A second SPB-associated scaffold, Cut12, promotes SPB-associated Cdk1-cyclin B to drive mitotic commitment. Signals emanating from each scaffold have been assumed to operate independently to promote two distinct outcomes. We now find that signals from Sid4 contribute to the Cut12 mitotic commitment switch. Specifically, phosphorylation of Sid4 by NIMAFin1 reduces Sid4 affinity for its SPB anchor, Ppc89, while also enhancing Sid4's affinity for casein kinase 1δ (CK1δ). The resulting phosphorylation of Sid4 by the newly docked CK1δ recruits Chk2Cds1 to Sid4. Chk2Cds1 then expels the Cdk1-cyclin B antagonistic phosphatase Flp1/Clp1 from the SPB. Flp1/Clp1 departure can then support mitotic commitment when Cdk1-cyclin B activation at the SPB is compromised by reduction of Cut12 function. Such integration of signals emanating from neighboring scaffolds shows how centrosomes/SPBs can integrate inputs from multiple pathways to control cell fate.
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Affiliation(s)
- Kuan Yoow Chan
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, England, UK
| | - Marisa Alonso-Nuñez
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, England, UK
| | - Agnes Grallert
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, England, UK
| | - Kayoko Tanaka
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, England, UK
| | - Yvonne Connolly
- Biological Mass Spectrometry Facility, Cancer Research UK Manchester Institute, University of Manchester, Manchester, England, UK
| | - Duncan L Smith
- Biological Mass Spectrometry Facility, Cancer Research UK Manchester Institute, University of Manchester, Manchester, England, UK
| | - Iain M Hagan
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, England, UK
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16
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Gruber W, Scheidt T, Aberger F, Huber CG. Understanding cell signaling in cancer stem cells for targeted therapy - can phosphoproteomics help to reveal the secrets? Cell Commun Signal 2017; 15:12. [PMID: 28356110 PMCID: PMC5372284 DOI: 10.1186/s12964-017-0166-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/13/2017] [Indexed: 12/11/2022] Open
Abstract
Background Cancer represents heterogeneous and aberrantly proliferative manifestations composed of (epi)genetically and phenotypically distinct cells with a common clonal origin. Cancer stem cells (CSC) make up a rare subpopulation with the remarkable capacity to initiate, propagate and spread a malignant disease. Furthermore, CSC show increased therapy resistance, thereby contributing to disease relapse. Elimination of CSC, therefore, is a crucial aim to design efficacious treatments for long-term survival of cancer patients. In this article, we highlight the nature of CSC and propose that phosphoproteomics based on unbiased high-performance liquid chromatography-mass spectrometry provides a powerful tool to decipher the molecular CSC programs. Detailed knowledge about the regulation of signaling processes in CSC is a prerequisite for the development of patient-tailored multi-modal treatments including the elimination of rare CSC. Main body Phosphorylation is a crucial post-translational modification regulating a plethora of both intra- and intercellular communication processes in normal and malignant cells. Small-molecule targeting of kinases has proven successful in the therapy, but the high rates of relapse and failure to stem malignant spread suggest that these kinase inhibitors largely spare CSC. Studying the kinetics of global phosphorylation patterns in an unbiased manner is, therefore, required to improve strategies and successful treatments within multi-modal therapeutic regimens by targeting the malignant behavior of CSC. The phosphoproteome comprises all phosphoproteins within a cell population that can be analyzed by phosphoproteomics, allowing the investigation of thousands of phosphorylation events. One major aspect is the perception of events underlying the activation and deactivation of kinases and phosphatases in oncogenic signaling pathways. Thus, not only can this tool be harnessed to better understand cellular processes such as those controlling CSC, but also applied to identify novel drug targets for targeted anti-CSC therapy. Conclusion State-of-the-art phosphoproteomics approaches focusing on single cell analysis have the potential to better understand oncogenic signaling in heterogeneous cell populations including rare, yet highly malignant CSC. By eliminating the influence of heterogeneity of populations, single-cell studies will reveal novel insights also into the inter- and intratumoral communication processes controlling malignant CSC and disease progression, laying the basis for improved rational combination treatments.
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Affiliation(s)
- Wolfgang Gruber
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Tamara Scheidt
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Fritz Aberger
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
| | - Christian G Huber
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
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17
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Grallert A, Hagan IM. Large-Scale Immunoprecipitation from Fission Yeast Cell Extracts. Cold Spring Harb Protoc 2017; 2017:2017/2/pdb.prot091595. [PMID: 28148853 DOI: 10.1101/pdb.prot091595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We outline immunoprecipitation (IP) procedures to isolate the large quantities of a molecule of interest that are required to identify posttranslational modifications (PTMs) in subsequent targeted mass spectrometry analysis. In situ denaturation by trichloroacetic acid precipitation inhibits the activities of modifying enzymes that could alter the PTM profile to preserve the PTMs on a target of interest throughout the precipitation step. In contrast, isolation of the same molecule with the nondenaturing variation on this IP procedure can maintain associations with partner molecules whose PTMs can also be mapped, albeit with the caveat that modifications could have occurred during the extended IP period.
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Affiliation(s)
- Agnes Grallert
- CRUK Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester M20 4BX, United Kingdom
| | - Iain M Hagan
- CRUK Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester M20 4BX, United Kingdom
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18
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Evolution of a mass spectrometry-grade protease with PTM-directed specificity. Proc Natl Acad Sci U S A 2016; 113:14686-14691. [PMID: 27940920 DOI: 10.1073/pnas.1609925113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mapping posttranslational modifications (PTMs), which diversely modulate biological functions, represents a significant analytical challenge. The centerpiece technology for PTM site identification, mass spectrometry (MS), requires proteolytic cleavage in the vicinity of a PTM to yield peptides for sequencing. This requirement catalyzed our efforts to evolve MS-grade mutant PTM-directed proteases. Citrulline, a PTM implicated in epigenetic and immunological function, made an ideal first target, because citrullination eliminates arginyl tryptic sites. Bead-displayed trypsin mutant genes were translated in droplets, the mutant proteases were challenged to cleave bead-bound fluorogenic probes of citrulline-dependent proteolysis, and the resultant beads (1.3 million) were screened. The most promising mutant efficiently catalyzed citrulline-dependent peptide bond cleavage (kcat/KM = 6.9 × 105 M-1⋅s-1). The resulting C-terminally citrullinated peptides generated characteristic isotopic patterns in MALDI-TOF MS, and both a fragmentation product y1 ion corresponding to citrulline (176.1030 m/z) and diagnostic peak pairs in the extracted ion chromatograms of LC-MS/MS analysis. Using these signatures, we identified citrullination sites in protein arginine deiminase 4 (12 sites) and in fibrinogen (25 sites, two previously unknown). The unique mass spectral features of PTM-dependent proteolytic digest products promise a generalized PTM site-mapping strategy based on a toolbox of such mutant proteases, which are now accessible by laboratory evolution.
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19
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Schacherer LJ, Xie W, Owens MA, Alarcon C, Hu TX. Rapid detection of proteins in transgenic crops without protein reference standards by targeted proteomic mass spectrometry. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:4116-4125. [PMID: 26750806 DOI: 10.1002/jsfa.7612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/09/2015] [Accepted: 01/05/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Liquid chromatography coupled with tandem mass spectrometry is increasingly used for protein detection for transgenic crops research. Currently this is achieved with protein reference standards which may take a significant time or efforts to obtain and there is a need for rapid protein detection without protein reference standards. RESULTS A sensitive and specific method was developed to detect target proteins in transgenic maize leaf crude extract at concentrations as low as ∼30 ng mg(-1) dry leaf without the need of reference standards or any sample enrichment. A hybrid Q-TRAP mass spectrometer was used to monitor all potential tryptic peptides of the target proteins in both transgenic and non-transgenic samples. The multiple reaction monitoring-initiated detection and sequencing (MIDAS) approach was used for initial peptide/protein identification via Mascot database search. Further confirmation was achieved by direct comparison between transgenic and non-transgenic samples. Definitive confirmation was provided by running the same experiments of synthetic peptides or protein standards, if available. CONCLUSION A targeted proteomic mass spectrometry method using MIDAS approach is an ideal methodology for detection of new proteins in early stages of transgenic crop research and development when neither protein reference standards nor antibodies are available. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Lindsey J Schacherer
- DuPont Pioneer Agricultural Biotechnology, 8325 Northwest 62nd Avenue, P.O. Box 7062, Johnston, Iowa, 50131, USA
| | - Weiping Xie
- DuPont Pioneer Agricultural Biotechnology, 4010 Point Eden Way, Hayward, California, 94545, USA
| | - Michaela A Owens
- DuPont Pioneer Agricultural Biotechnology, 8325 Northwest 62nd Avenue, P.O. Box 7062, Johnston, Iowa, 50131, USA
| | - Clara Alarcon
- DuPont Pioneer Agricultural Biotechnology, 8325 Northwest 62nd Avenue, P.O. Box 7062, Johnston, Iowa, 50131, USA
| | - Tiger X Hu
- DuPont Pioneer Agricultural Biotechnology, 8325 Northwest 62nd Avenue, P.O. Box 7062, Johnston, Iowa, 50131, USA
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20
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Szász AM, Győrffy B, Marko-Varga G. Cancer heterogeneity determined by functional proteomics. Semin Cell Dev Biol 2016; 64:132-142. [PMID: 27569188 DOI: 10.1016/j.semcdb.2016.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/24/2016] [Indexed: 01/04/2023]
Abstract
Current manuscript gives a synopsis of tumor heterogeneity related to patient samples analyzed by proteomics, protein expression analysis and imaging mass spectrometry. First, we discuss the pathophysiologocal background of cancer biology as a multifactorial and challenging diseases. Disease pathology forms the basis for protein target selection. Therefore, histopathological diagnostics and grading of tumors is highlighted. Pathology is the cornerstone of state-of-the-art diagnostics of tumors today both by establishing dignity and - when needed - describing molecular properties of the cancers. Drug development by the pharmaceutical industry utilizes proteomics studies to pinpoint the most relevant targets. Molecular studies profiling affinity-interactions of the protein(s) with targeted small drug molecules to reach efficacy and optimal patient safety are today requested by the FDA and other agencies for new drug development. An understading of basic mechanisms, controlling drug action and drug binding is central, as a new era of personalized medicine becomes an important milestone solution for the healthcare sector as well as the Pharma and Biotech industry. Development of further diagnostic, prognostic and predictive tests will aid current and future treatment of cancer patients. In the paper we present current status of Proteomics that we believe requires attention in order to collectively advance forward in the fight against cancer, addressing the burning opportunities and challenges.
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Affiliation(s)
- A Marcell Szász
- MTA-TTK Lendület Cancer Biomarker Research Group, Hungarian Academy of Sciences, 1117 Budapest, Hungary; Second Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; Centre of Excellence in Biological and Medical Mass Spectrometry, Biomedical Centre D13, Lund University, 221 84 Lund, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Balázs Győrffy
- MTA-TTK Lendület Cancer Biomarker Research Group, Hungarian Academy of Sciences, 1117 Budapest, Hungary; Second Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - György Marko-Varga
- Centre of Excellence in Biological and Medical Mass Spectrometry, Biomedical Centre D13, Lund University, 221 84 Lund, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; First Department of Surgery, Tokyo Medical University, Tokyo, 160-0023 Japan.
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21
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Schmidlin T, Garrigues L, Lane CS, Mulder TC, van Doorn S, Post H, de Graaf EL, Lemeer S, Heck AJR, Altelaar AFM. Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non-small cell lung cancer. Proteomics 2016; 16:2193-205. [DOI: 10.1002/pmic.201500453] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/12/2016] [Accepted: 05/20/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Thierry Schmidlin
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Luc Garrigues
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | | | - T. Celine Mulder
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Erik L. de Graaf
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
- Current address: Erik L. de Graaf, Fondazione Pisana per la Scienza ONLUS; Via Panfilo Castaldi 2; 56121 Pisa Italy
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - A. F. Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
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22
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Tao H, Zhang Y, Cao X, Deng Z, Liu T. Absolute quantification of proteins in the fatty acid biosynthetic pathway using protein standard absolute quantification. Synth Syst Biotechnol 2016; 1:150-157. [PMID: 29062939 PMCID: PMC5640790 DOI: 10.1016/j.synbio.2016.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/30/2015] [Accepted: 01/03/2016] [Indexed: 11/24/2022] Open
Abstract
With worldwide attention on renewable energy and climate change, metabolic engineering of the fatty acid biosynthetic pathway has become an active area of research, with a view to enhance production of biofuels. Indeed, this pathway has already been extensively studied in Escherichia coli. Nevertheless, little is known about the absolute abundance of the enzymes involved, information that may be valuable for engineering, such as the optimal molar ratios of different proteins. In this study, we use protein standard absolute quantification (PSAQ) to measure the absolute abundance of proteins that catalyze fatty acid biosynthesis in E. coli. In addition, the changes of protein abundance were analyzed by comparing the differences between high-yield and the background strain. Our work highlights opportunities to enhance fatty acid production by measuring protein molar ratios and identifying catalytic and regulatory bottlenecks. More importantly, our results provide evidence that PSAQ is a generally valuable tool to investigate metabolic pathways.
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Affiliation(s)
- Hui Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, P.R. China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, P.R. China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, P.R. China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, P.R. China
| | - Xiaoying Cao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, P.R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, P.R. China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, P.R. China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, P.R. China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, P.R. China.,Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan 430068, P.R. China
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23
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Heaven MR, Funk AJ, Cobbs AL, Haffey WD, Norris JL, McCullumsmith RE, Greis KD. Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics-a prototype design for a single injection assay. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1-11. [PMID: 26757066 PMCID: PMC4712743 DOI: 10.1002/jms.3716] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/02/2015] [Accepted: 10/11/2015] [Indexed: 06/05/2023]
Abstract
Data-independent acquisition (DIA)-based proteomics has become increasingly complicated in recent years because of the vast number of workflows described, coupled with a lack of studies indicating a rational framework for selecting effective settings to use. To address this issue and provide a resource for the proteomics community, we compared 12 DIA methods that assay tryptic peptides using various mass-isolation windows. Our findings indicate that the most sensitive single injection LC-DIA method uses 6 m/z isolation windows to analyze the densely populated tryptic peptide range from 450 to 730 m/z, which allowed quantification of 4465 Escherichia coli peptides. In contrast, using the sequential windowed acquisition of all theoretical fragment-ions (SWATH) approach with 26 m/z isolation windows across the entire 400-1200 m/z range, allowed quantification of only 3309 peptides. This reduced sensitivity with 26 m/z windows is caused by an increase in co-eluting compounds with similar precursor values detected in the same tandem MS spectra, which lowers the signal-to-noise of peptide fragment-ion chromatograms and reduces the amount of low abundance peptides that can be quantified from 410 to 920 m/z. Above 920 m/z, more peptides were quantified with 26 m/z windows because of substantial peptide (13) C isotope distributions that parse peptide ions into separate isolation windows. Because reproducible quantification has been a long-standing aim of quantitative proteomics, and is a so-called trait of DIA, we sought to determine whether precursor-level chromatograms used in some methods rather than their fragment-level counterparts have similar precision. Our data show that extracted fragment-ion chromatograms are the reason DIA provides superior reproducibility. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Adam J. Funk
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | | | - Wendy D. Haffey
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Jeremy L. Norris
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Robert E. McCullumsmith
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Kenneth D. Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
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24
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Damerill I, Biggar KK, Abu Shehab M, Li SSC, Jansson T, Gupta MB. Hypoxia Increases IGFBP-1 Phosphorylation Mediated by mTOR Inhibition. Mol Endocrinol 2015; 30:201-16. [PMID: 26714229 DOI: 10.1210/me.2015-1194] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In fetal growth restriction (FGR), fetal growth is limited by reduced nutrient and oxygen supply. Insulin-like growth factor I (IGF-I) is a key regulator of fetal growth and IGF binding protein -1(IGFBP-1) is the principal regulator of fetal IGF-I bioavailability. Phosphorylation enhances IGFBP-1's affinity for IGF-I. Hypoxia induces IGFBP-1 hyperphosphorylation, markedly decreasing IGF-I bioavailability. We recently reported that fetal liver IGFBP-1 hyperphosphorylation is associated with inhibition of the mechanistic target of rapamycin (mTOR) in a nonhuman primate model of FGR. Here, we test the hypothesis that IGFBP-1 hyperphosphorylation in response to hypoxia is mediated by mTOR inhibition. We inhibited mTOR either by rapamycin or small interfering RNA (siRNA) targeting raptor (mTOR complex [mTORC]1) and/or rictor (mTORC2) in HepG2 cells cultured under hypoxia (1% O2) or basal (20% O2) conditions. Conversely, we activated mTORC1 or mTORC1+mTORC2 by silencing endogenous mTOR inhibitors (tuberous sclerosis complex 2/DEP-domain-containing and mTOR-interacting protein). Immunoblot analysis demonstrated that both hypoxia and inhibition of mTORC1 and/or mTORC2 induced similar degrees of IGFBP-1 phosphorylation at Ser101/119/169 and reduced IGF-I receptor autophosphorylation. Activation of mTORC1+mTORC2 or mTORC1 alone prevented IGFBP-1 hyperphosphorylation in response to hypoxia. Multiple reaction monitoring-mass spectrometry showed that rapamycin and/or hypoxia increased phosphorylation also at Ser98 and at a novel site Ser174. In silico structural analysis indicated that Ser174 was in close proximity to the IGF-binding site. Together, we demonstrate that signaling through the mTORC1 or mTORC2 pathway is sufficient to induce IGFBP-1 hyperphosphorylation in response to hypoxia. This study provides novel understanding of the cellular mechanism that controls fetal IGFBP-1 phosphorylation in hypoxia, and we propose that mTOR inhibition constitutes a mechanistic link between hypoxia, reduced IGF-I bioavailability and FGR.
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Affiliation(s)
- Ian Damerill
- Department of Biochemistry (I.D., K.K.B., S.S.-C.L., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada; Department of Obstetrics and Gynecology (T.J.), University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Pediatrics (M.B.G.), University of Western Ontario, London, N6C 2V5 Canada; and Children's Health Research Institute (M.A.S., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada
| | - Kyle K Biggar
- Department of Biochemistry (I.D., K.K.B., S.S.-C.L., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada; Department of Obstetrics and Gynecology (T.J.), University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Pediatrics (M.B.G.), University of Western Ontario, London, N6C 2V5 Canada; and Children's Health Research Institute (M.A.S., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada
| | - Majida Abu Shehab
- Department of Biochemistry (I.D., K.K.B., S.S.-C.L., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada; Department of Obstetrics and Gynecology (T.J.), University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Pediatrics (M.B.G.), University of Western Ontario, London, N6C 2V5 Canada; and Children's Health Research Institute (M.A.S., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada
| | - Shawn Shun-Cheng Li
- Department of Biochemistry (I.D., K.K.B., S.S.-C.L., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada; Department of Obstetrics and Gynecology (T.J.), University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Pediatrics (M.B.G.), University of Western Ontario, London, N6C 2V5 Canada; and Children's Health Research Institute (M.A.S., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada
| | - Thomas Jansson
- Department of Biochemistry (I.D., K.K.B., S.S.-C.L., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada; Department of Obstetrics and Gynecology (T.J.), University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Pediatrics (M.B.G.), University of Western Ontario, London, N6C 2V5 Canada; and Children's Health Research Institute (M.A.S., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada
| | - Madhulika B Gupta
- Department of Biochemistry (I.D., K.K.B., S.S.-C.L., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada; Department of Obstetrics and Gynecology (T.J.), University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Pediatrics (M.B.G.), University of Western Ontario, London, N6C 2V5 Canada; and Children's Health Research Institute (M.A.S., M.B.G.), University of Western Ontario, London, Ontario, N6C 2V5 Canada
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25
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Mageean CJ, Griffiths JR, Smith DL, Clague MJ, Prior IA. Absolute Quantification of Endogenous Ras Isoform Abundance. PLoS One 2015; 10:e0142674. [PMID: 26560143 PMCID: PMC4641634 DOI: 10.1371/journal.pone.0142674] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/26/2015] [Indexed: 01/15/2023] Open
Abstract
Ras proteins are important signalling hubs situated near the top of networks controlling cell proliferation, differentiation and survival. Three almost identical isoforms, HRAS, KRAS and NRAS, are ubiquitously expressed yet have differing biological and oncogenic properties. In order to help understand the relative biological contributions of each isoform we have optimised a quantitative proteomics method for accurately measuring Ras isoform protein copy number per cell. The use of isotopic protein standards together with selected reaction monitoring for diagnostic peptides is sensitive, robust and suitable for application to sub-milligram quantities of lysates. We find that in a panel of isogenic SW48 colorectal cancer cells, endogenous Ras proteins are highly abundant with ≥260,000 total Ras protein copies per cell and the rank order of isoform abundance is KRAS>NRAS≥HRAS. A subset of oncogenic KRAS mutants exhibit increased total cellular Ras abundance and altered the ratio of mutant versus wild type KRAS protein. These data and methodology are significant because Ras protein copy number is required to parameterise models of signalling networks and informs interpretation of isoform-specific Ras functional data.
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Affiliation(s)
- Craig J. Mageean
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom
| | - John R. Griffiths
- Cancer Research UK Manchester Institute, University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Duncan L. Smith
- Cancer Research UK Manchester Institute, University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Michael J. Clague
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom
| | - Ian A. Prior
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom
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26
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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27
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Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. J Proteomics 2015; 126:24-33. [DOI: 10.1016/j.jprot.2015.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/13/2015] [Accepted: 05/20/2015] [Indexed: 12/25/2022]
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28
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Whalley HJ, Porter AP, Diamantopoulou Z, White GRM, Castañeda-Saucedo E, Malliri A. Cdk1 phosphorylates the Rac activator Tiam1 to activate centrosomal Pak and promote mitotic spindle formation. Nat Commun 2015; 6:7437. [PMID: 26078008 PMCID: PMC4490568 DOI: 10.1038/ncomms8437] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 05/08/2015] [Indexed: 01/13/2023] Open
Abstract
Centrosome separation is critical for bipolar spindle formation and the accurate segregation of chromosomes during mammalian cell mitosis. Kinesin-5 (Eg5) is a microtubule motor essential for centrosome separation, and Tiam1 and its substrate Rac antagonize Eg5-dependent centrosome separation in early mitosis promoting efficient chromosome congression. Here we identify S1466 of Tiam1 as a novel Cdk1 site whose phosphorylation is required for the mitotic function of Tiam1. We find that this phosphorylation of Tiam1 is required for the activation of group I p21-activated kinases (Paks) on centrosomes in prophase. Further, we show that both Pak1 and Pak2 counteract centrosome separation in a kinase-dependent manner and demonstrate that they act downstream of Tiam1. We also show that depletion of Pak1/2 allows cells to escape monopolar arrest by Eg5 inhibition, highlighting the potential importance of this signalling pathway for the development of Eg5 inhibitors as cancer therapeutics.
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Affiliation(s)
- Helen J. Whalley
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Andrew P. Porter
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Zoi Diamantopoulou
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Gavin R. M. White
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Eduardo Castañeda-Saucedo
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Angeliki Malliri
- Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
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29
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López-Villar E, Martos-Moreno GÁ, Chowen JA, Okada S, Kopchick JJ, Argente J. A proteomic approach to obesity and type 2 diabetes. J Cell Mol Med 2015; 19:1455-70. [PMID: 25960181 PMCID: PMC4511345 DOI: 10.1111/jcmm.12600] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/02/2015] [Indexed: 12/13/2022] Open
Abstract
The incidence of obesity and type diabetes 2 has increased dramatically resulting in an increased interest in its biomedical relevance. However, the mechanisms that trigger the development of diabetes type 2 in obese patients remain largely unknown. Scientific, clinical and pharmaceutical communities are dedicating vast resources to unravel this issue by applying different omics tools. During the last decade, the advances in proteomic approaches and the Human Proteome Organization have opened and are opening a new door that may be helpful in the identification of patients at risk and to improve current therapies. Here, we briefly review some of the advances in our understanding of type 2 diabetes that have occurred through the application of proteomics. We also review, in detail, the current improvements in proteomic methodologies and new strategies that could be employed to further advance our understanding of this pathology. By applying these new proteomic advances, novel therapeutic and/or diagnostic protein targets will be discovered in the obesity/Type 2 diabetes area.
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Affiliation(s)
- Elena López-Villar
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Oncohematology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Gabriel Á Martos-Moreno
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie A Chowen
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Shigeru Okada
- Edison Biotechnology Institute, Ohio University, Konneker Research Laboratories, Athens, OH, USA.,Department of Pediatrics, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Konneker Research Laboratories, Athens, OH, USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH, USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Jesús Argente
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
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30
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Gallien S, Kim SY, Domon B. Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM). Mol Cell Proteomics 2015; 14:1630-44. [PMID: 25755295 DOI: 10.1074/mcp.o114.043968] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 12/22/2022] Open
Abstract
Targeted high-resolution and accurate mass analyses performed on fast sequencing mass spectrometers have opened new avenues for quantitative proteomics. More specifically, parallel reaction monitoring (PRM) implemented on quadrupole-orbitrap instruments exhibits exquisite selectivity to discriminate interferences from analytes. Furthermore, the instrument trapping capability enhances the sensitivity of the measurements. The PRM technique, applied to the analysis of limited peptide sets (typically 50 peptides or less) in a complex matrix, resulted in an improved detection and quantification performance as compared with the reference method of selected reaction monitoring performed on triple quadrupole instruments. However, the implementation of PRM for the analysis of large peptide numbers requires the adjustment of mass spectrometry acquisition parameters, which affects dramatically the quality of the generated data, and thus the overall output of an experiment. A newly designed data acquisition scheme enabled the analysis of moderate-to-large peptide numbers while retaining a high performance level. This new method, called internal standard triggered-parallel reaction monitoring (IS-PRM), relies on added internal standards and the on-the-fly adjustment of acquisition parameters to drive in real-time measurement of endogenous peptides. The acquisition time management was designed to maximize the effective time devoted to measure the analytes in a time-scheduled targeted experiment. The data acquisition scheme alternates between two PRM modes: a fast low-resolution "watch mode" and a "quantitative mode" using optimized parameters ensuring data quality. The IS-PRM method exhibited a highly effective use of the instrument time. Applied to the analysis of large peptide sets (up to 600) in complex samples, the method showed an unprecedented combination of scale and analytical performance, with limits of quantification in the low amol range. The successful analysis of various types of biological samples augurs a broad applicability of the method, which is likely to benefit a wide range of proteomics experiments.
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Affiliation(s)
- Sebastien Gallien
- From the ‡Luxembourg Clinical Proteomics Center (LCP), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Sang Yoon Kim
- From the ‡Luxembourg Clinical Proteomics Center (LCP), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Bruno Domon
- From the ‡Luxembourg Clinical Proteomics Center (LCP), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
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31
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Timm T, Lenz C, Merkel D, Sadiffo C, Grabitzki J, Klein J, Lochnit G. Detection and site localization of phosphorylcholine-modified peptides by NanoLC-ESI-MS/MS using precursor ion scanning and multiple reaction monitoring experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:460-471. [PMID: 25487775 DOI: 10.1007/s13361-014-1036-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/17/2014] [Accepted: 10/22/2014] [Indexed: 06/04/2023]
Abstract
Phosphorylcholine (PC)-modified biomolecules like lipopolysaccharides, glycosphingolipids, and (glyco)proteins are widespread, highly relevant antigens of parasites, since this small hapten shows potent immunomodulatory capacity, which allows the establishment of long-lasting infections of the host. Especially for PC-modified proteins, structural data is rare because of the zwitterionic nature of the PC substituent, resulting in low sensitivities and unusual but characteristic fragmentation patterns. We have developed a targeted mass spectrometric approach using hybrid triple quadrupole/linear ion trap (QTRAP) mass spectrometry coupled to nanoflow chromatography for the sensitive detection of PC-modified peptides from complex proteolytic digests, and the localization of the PC-modification within the peptide backbone. In a first step, proteolytic digests are screened using precursor ion scanning for the marker ions of choline (m/z 104.1) and phosphorylcholine (m/z 184.1) to establish the presence of PC-modified peptides. Potential PC-modified precursors are then subjected to a second analysis using multiple reaction monitoring (MRM)-triggered product ion spectra for the identification and site localization of the modified peptides. The approach was first established using synthetic PC-modified synthetic peptides and PC-modified model digests. Following the optimization of key parameters, we then successfully applied the method to the detection of PC-peptides in the background of a proteolytic digest of a whole proteome. This methodological invention will greatly facilitate the detection of PC-substituted biomolecules and their structural analysis.
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Affiliation(s)
- Thomas Timm
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University Giessen, 35392, Giessen, Germany
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32
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Goldman R, Sanda M. Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clin Appl 2015; 9:17-32. [PMID: 25522218 PMCID: PMC5780646 DOI: 10.1002/prca.201400152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/15/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated.
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Affiliation(s)
- Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
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33
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Automatisierte Detektion von Proteinphosphorylierung durch Nanoliter-Enzymreaktionen auf Mikroarrays. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Screening for protein phosphorylation using nanoscale reactions on microdroplet arrays. Angew Chem Int Ed Engl 2014; 54:1671-5. [PMID: 25504774 DOI: 10.1002/anie.201409440] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/25/2022]
Abstract
We present a novel and straightforward screening method to detect protein phosphorylations in complex protein mixtures. A proteolytic digest is separated by a conventional nanoscale liquid chromatography (nano-LC) separation and the eluate is immediately compartmentalized into microdroplets, which are spotted on a microarray MALDI plate. Subsequently, the enzyme alkaline phosphatase is applied to every second microarray spot to remove the phosphate groups from phosphorylated peptides, which results in a mass shift of n×-80 Da. The MALDI-MS scan of the microarray is then evaluated by a software algorithm to automatically identify the phosphorylated peptides by exploiting the characteristic chromatographic peak profile induced by the phosphatase treatment. This screening method does not require extensive MS/MS experiments or peak list evaluation and can be easily extended to other enzymatic or chemical reactions.
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Affiliation(s)
- Simon K Küster
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich (Switzerland)
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35
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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36
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Gianazza E, Tremoli E, Banfi C. The selected reaction monitoring/multiple reaction monitoring-based mass spectrometry approach for the accurate quantitation of proteins: clinical applications in the cardiovascular diseases. Expert Rev Proteomics 2014; 11:771-88. [PMID: 25400095 DOI: 10.1586/14789450.2014.947966] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Selected reaction monitoring, also known as multiple reaction monitoring, is a powerful targeted mass spectrometry approach for a confident quantitation of proteins/peptides in complex biological samples. In recent years, its optimization and application have become pivotal and of great interest in clinical research to derive useful outcomes for patient care. Thus, selected reaction monitoring/multiple reaction monitoring is now used as a highly sensitive and selective method for the evaluation of protein abundances and biomarker verification with potential applications in medical screening. This review describes technical aspects for the development of a robust multiplex assay and discussing its recent applications in cardiovascular proteomics: verification of promising disease candidates to select only the highest quality peptides/proteins for a preclinical validation, as well as quantitation of protein isoforms and post-translational modifications.
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Affiliation(s)
- Erica Gianazza
- Laboratory of Cell Biology and Biochemistry of Atherothrombosis, Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Via Parea 4, 20138 Milan, Italy
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37
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Ramirez-Correa GA, Martinez-Ferrando MI, Zhang P, Murphy AM. Targeted proteomics of myofilament phosphorylation and other protein posttranslational modifications. Proteomics Clin Appl 2014; 8:543-53. [DOI: 10.1002/prca.201400034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/29/2014] [Accepted: 06/24/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Genaro A. Ramirez-Correa
- Department of Pediatrics/Division of Cardiology; Johns Hopkins University School of Medicine; Baltimore MD USA
| | | | - Pingbo Zhang
- The Hopkins Bayview Proteomics Center; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Anne M. Murphy
- Department of Pediatrics/Division of Cardiology; Johns Hopkins University School of Medicine; Baltimore MD USA
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38
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Hammond TG, Meng X, Jenkins RE, Maggs JL, Castelazo AS, Regan SL, Bennett SNL, Earnshaw CJ, Aithal GP, Pande I, Kenna JG, Stachulski AV, Park BK, Williams DP. Mass spectrometric characterization of circulating covalent protein adducts derived from a drug acyl glucuronide metabolite: multiple albumin adductions in diclofenac patients. J Pharmacol Exp Ther 2014; 350:387-402. [PMID: 24902585 PMCID: PMC4109494 DOI: 10.1124/jpet.114.215079] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/29/2014] [Indexed: 12/21/2022] Open
Abstract
Covalent protein modifications by electrophilic acyl glucuronide (AG) metabolites are hypothetical causes of hypersensitivity reactions associated with certain carboxylate drugs. The complex rearrangements and reactivities of drug AG have been defined in great detail, and protein adducts of carboxylate drugs, such as diclofenac, have been found in liver and plasma of experimental animals and humans. However, in the absence of definitive molecular characterization, and specifically, identification of signature glycation conjugates retaining the glucuronyl and carboxyl residues, it cannot be assumed any of these adducts is derived uniquely or even fractionally from AG metabolites. We have therefore undertaken targeted mass spectrometric analyses of human serum albumin (HSA) isolated from diclofenac patients to characterize drug-: derived structures and, thereby, for the first time, have deconstructed conclusively the pathways of adduct formation from a drug AG and its isomeric rearrangement products in vivo. These analyses were informed by a thorough understanding of the reactions of HSA with diclofenac AG in vitro. HSA from six patients without drug-: related hypersensitivities had either a single drug-: derived adduct or one of five combinations of 2-8 adducts from among seven diclofenac N-acylations and three AG glycations on seven of the protein's 59 lysines. Only acylations were found in every patient. We present evidence that HSA modifications by diclofenac in vivo are complicated and variable, that at least a fraction of these modifications are derived from the drug's AG metabolite, and that albumin adduction is not inevitably a causation of hypersensitivity to carboxylate drugs or a coincidental association.
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Affiliation(s)
- Thomas G Hammond
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Xiaoli Meng
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Rosalind E Jenkins
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - James L Maggs
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Anahi Santoyo Castelazo
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Sophie L Regan
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Stuart N L Bennett
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Caroline J Earnshaw
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Guruprasad P Aithal
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Ira Pande
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - J Gerry Kenna
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Andrew V Stachulski
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - B Kevin Park
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Dominic P Williams
- Medical Research Council Centre for Drug Safety Science, Institute of Translational Medicine, (T.G.H., X.M., R.E.J., J.L.M., A.S.C., S.L.R., C.J.E., B.K.P., D.P.W.) and Department of Chemistry (A.V.S.), University of Liverpool, Liverpool, United Kingdom; Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases-Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham (G.P.A.) and Department of Rheumatology, Nottingham University Hospitals NHS Trust (I.P.), Nottingham, United Kingdom; and AstraZeneca U.K. Ltd (S.N.L.B.) and Safety Assessment, AstraZeneca U.K. Ltd (J.G.K.), Alderley Park, Macclesfield, Cheshire, United Kingdom
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Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 2014; 10:551-66. [PMID: 24206228 DOI: 10.1586/14789450.2013.858022] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. These methods hold promises to address the shortcomings of data-dependent analysis and selected reaction monitoring (SRM) employed in shotgun and targeted proteomics, respectively. They allow MS analyses of all species in a complex sample indiscriminately, or permit SRM-like experiments conducted with full high-resolution product ion spectra, potentially leading to higher sequence coverage or analytical selectivity. These methods include MS(E), all-ion fragmentation, Fourier transform-all reaction monitoring, SWATH Acquisition, multiplexed MS/MS, pseudo-SRM (pSRM) and parallel reaction monitoring (PRM). In this review, the strengths and pitfalls of these methods are discussed and illustrated with examples. In essence, the suitability of the use of each method is contingent on the biological questions posed. Although these methods do not fundamentally change the shape of proteomics, they are useful additional tools that should expedite biological discoveries.
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Affiliation(s)
- Kai Pong Law
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD4, Level 1, 14 Medical Drive, 117599, Singapore
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40
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Kelstrup CD, Frese C, Heck AJR, Olsen JV, Nielsen ML. Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID). Mol Cell Proteomics 2014; 13:1914-24. [PMID: 24895383 PMCID: PMC4125726 DOI: 10.1074/mcp.o113.035915] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Unambiguous identification of tandem mass spectra is a cornerstone in mass-spectrometry-based proteomics. As the study of post-translational modifications (PTMs) by means of shotgun proteomics progresses in depth and coverage, the ability to correctly identify PTM-bearing peptides is essential, increasing the demand for advanced data interpretation. Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. Although such ions offer tremendous analytical advantages, algorithms to decipher MS/MS spectra for the presence of diagnostic ions in an unbiased manner are currently lacking. Here, we present a systematic spectral-pattern-based approach for the discovery of diagnostic ions and new fragmentation mechanisms in shotgun proteomics datasets. The developed software tool is designed to analyze large sets of high-resolution peptide fragmentation spectra independent of the fragmentation method, instrument type, or protease employed. To benchmark the software tool, we analyzed large higher-energy collisional activation dissociation datasets of samples containing phosphorylation, ubiquitylation, SUMOylation, formylation, and lysine acetylation. Using the developed software tool, we were able to identify known diagnostic ions by comparing histograms of modified and unmodified peptide spectra. Because the investigated tandem mass spectra data were acquired with high mass accuracy, unambiguous interpretation and determination of the chemical composition for the majority of detected fragment ions was feasible. Collectively we present a freely available software tool that allows for comprehensive and automatic analysis of analogous product ions in tandem mass spectra and systematic mapping of fragmentation mechanisms related to common amino acids.
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Affiliation(s)
- Christian D Kelstrup
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark
| | - Christian Frese
- §Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Albert J R Heck
- §Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Jesper V Olsen
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark
| | - Michael L Nielsen
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark;
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You J, Willcox MD, Madigan MC, Wasinger V, Schiller B, Walsh BJ, Graham PH, Kearsley JH, Li Y. Tear fluid protein biomarkers. Adv Clin Chem 2014; 62:151-96. [PMID: 24772667 DOI: 10.1016/b978-0-12-800096-0.00004-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The tear film covers and protects the ocular surface. It contains various molecules including a large variety of proteins. The protein composition of the tear fluid can change with respect to various local and systemic diseases. Prior to the advent of the proteomic era, tear protein analysis was limited to a few analytical techniques, the most common of which was immunoelectrophoresis, an approach dependent on antibody availability. Using proteomics, hundreds of tear proteins could potentially be identified and subsequently studied. Although detection of low-abundance proteins in the complex tear proteome remains a challenge, advances in sample fractionation and mass spectrometry have greatly enhanced our ability to detect these proteins. With increasing proteomic applications, tears show great potential as biomarkers in the development of clinical assays for various human diseases. In this chapter, we discuss the structure and functions of the tear film and methods for its collection. We also summarize potential tear protein biomarkers identified using proteomic techniques for both ocular and systemic diseases. Finally, modern proteomic techniques for tear biomarker research and future challenges are explored.
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42
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Percy AJ, Simon R, Chambers AG, Borchers CH. Enhanced sensitivity and multiplexing with 2D LC/MRM-MS and labeled standards for deeper and more comprehensive protein quantitation. J Proteomics 2014; 106:113-24. [PMID: 24769237 DOI: 10.1016/j.jprot.2014.04.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 04/10/2014] [Accepted: 04/14/2014] [Indexed: 01/04/2023]
Abstract
UNLABELLED Mass spectrometry (MS)-based protein quantitation is increasingly being employed to verify candidate protein biomarkers. Multiple or selected reaction monitoring-mass spectrometry (MRM-MS or SRM-MS) with isotopically labeled internal standards has proven to be a successful approach in that regard, but has yet to reach its full potential in terms of multiplexing and sensitivity. Here, we report the development of a new MRM method for the quantitation of 253 disease-associated proteins (represented by 625 interference-free peptides) in 13 LC fractions. This 2D RPLC/MRM-MS approach extends the depth and breadth of the assay by 2 orders of magnitude over pre-fractionation-free assays, with 31 proteins below 10 ng/mL and 41 proteins above 10 ng/mL now quantifiable. Standard flow rates are used in both chromatographic dimensions, and up-front depletion or antibody-based enrichment is not required. The LC separations utilize high and low pH conditions, with the former employing an ammonium hydroxide-based eluent, instead of the conventional ammonium formate, resulting in improved LC column lifetime and performance. The high sensitivity (determined concentration range: 15 mg/mL to 452 pg/mL) and robustness afforded by this method makes the full MRM panel, or subsets thereof, useful for the verification of disease-associated plasma protein biomarkers in patient samples. BIOLOGICAL SIGNIFICANCE The described research extends the breadth and depth of protein quantitation in undepleted and non-enriched human plasma by employing standard-flow 2D RPLC/MRM-MS in conjunction with a complex mixture of isotopically labeled peptide standards. The proteins quantified are mainly putative biomarkers of non-communicable (i.e., non-infectious) disease (e.g., cardiovascular or cancer), which require pre-clinical verification and validation before clinical implementation. Based on the enhanced sensitivity and multiplexing, this quantitative plasma proteomic method should prove useful in future candidate biomarker verification studies.
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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
| | - Romain Simon
- 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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Ansari D, Aronsson L, Sasor A, Welinder C, Rezeli M, Marko-Varga G, Andersson R. The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science. J Transl Med 2014; 12:87. [PMID: 24708694 PMCID: PMC3998064 DOI: 10.1186/1479-5876-12-87] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
In the post-genomic era, it has become evident that genetic changes alone are not sufficient to understand most disease processes including pancreatic cancer. Genome sequencing has revealed a complex set of genetic alterations in pancreatic cancer such as point mutations, chromosomal losses, gene amplifications and telomere shortening that drive cancerous growth through specific signaling pathways. Proteome-based approaches are important complements to genomic data and provide crucial information of the target driver molecules and their post-translational modifications. By applying quantitative mass spectrometry, this is an alternative way to identify biomarkers for early diagnosis and personalized medicine. We review the current quantitative mass spectrometric technologies and analyses that have been developed and applied in the last decade in the context of pancreatic cancer. Examples of candidate biomarkers that have been identified from these pancreas studies include among others, asporin, CD9, CXC chemokine ligand 7, fibronectin 1, galectin-1, gelsolin, intercellular adhesion molecule 1, insulin-like growth factor binding protein 2, metalloproteinase inhibitor 1, stromal cell derived factor 4, and transforming growth factor beta-induced protein. Many of these proteins are involved in various steps in pancreatic tumor progression including cell proliferation, adhesion, migration, invasion, metastasis, immune response and angiogenesis. These new protein candidates may provide essential information for the development of protein diagnostics and targeted therapies. We further argue that new strategies must be advanced and established for the integration of proteomic, transcriptomic and genomic data, in order to enhance biomarker translation. Large scale studies with meta data processing will pave the way for novel and unexpected correlations within pancreatic cancer, that will benefit the patient, with targeted treatment.
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Affiliation(s)
| | | | | | | | | | | | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University, and Skåne University Hospital, SE-221 85 Lund, Sweden.
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Gallien S, Bourmaud A, Kim SY, Domon B. Technical considerations for large-scale parallel reaction monitoring analysis. J Proteomics 2014; 100:147-59. [DOI: 10.1016/j.jprot.2013.10.029] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 09/26/2013] [Accepted: 10/21/2013] [Indexed: 11/28/2022]
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Licona-Cassani C, Lim S, Marcellin E, Nielsen LK. Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome. Mol Cell Proteomics 2014; 13:1219-30. [PMID: 24615062 DOI: 10.1074/mcp.m113.033951] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Actinomycetes undergo a dramatic reorganization of metabolic and cellular machinery during a brief period of growth arrest ("metabolic switch") preceding mycelia differentiation and the onset of secondary metabolite biosynthesis. This study explores the role of phosphorylation in coordinating the metabolic switch in the industrial actinomycete Saccharopolyspora erythraea. A total of 109 phosphopeptides from 88 proteins were detected across a 150-h fermentation using open-profile two-dimensional LC-MS proteomics and TiO(2) enrichment. Quantitative analysis of the phosphopeptides and their unphosphorylated cognates was possible for 20 pairs that also displayed constant total protein expression. Enzymes from central carbon metabolism such as putative acetyl-coenzyme A carboxylase, isocitrate lyase, and 2-oxoglutarate dehydrogenase changed dramatically in the degree of phosphorylation during the stationary phase, suggesting metabolic rearrangement for the reutilization of substrates and the production of polyketide precursors. In addition, an enzyme involved in cellular response to environmental stress, trypsin-like serine protease (SACE_6340/NC_009142_6216), decreased in phosphorylation during the growth arrest stage. More important, enzymes related to the regulation of protein synthesis underwent rapid phosphorylation changes during this stage. Whereas the degree of phosphorylation of ribonuclease Rne/Rng (SACE_1406/NC_009142_1388) increased during the metabolic switch, that of two ribosomal proteins, S6 (SACE_7351/NC_009142_7233) and S32 (SACE_6101/NC_009142_5981), dramatically decreased during this stage of the fermentation, supporting the hypothesis that ribosome subpopulations differentially regulate translation before and after the metabolic switch. Overall, we show the great potential of phosphoproteomic studies to explain microbial physiology and specifically provide evidence of dynamic protein phosphorylation events across the developmental cycle of actinomycetes.
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Affiliation(s)
- Cuauhtemoc Licona-Cassani
- §Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD 4072, Australia
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Ackermann BL, Berna MJ. Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev Proteomics 2014; 4:175-86. [PMID: 17425454 DOI: 10.1586/14789450.4.2.175] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The field of proteomics is rapidly turning towards targeted mass spectrometry (MS) methods to quantify putative markers or known proteins of biological interest. Historically, the enzyme-linked immunosorbent assay (ELISA) has been used for targeted protein analysis, but, unfortunately, it is limited by the excessive time required for antibody preparation, as well as concerns over selectivity. Despite the ability of proteomics to deliver increasingly quantitative measurements, owing to limited sensitivity, the leads generated are in the microgram per milliliter range. This stands in stark contrast to ELISA, which is capable of quantifying proteins at low picogram per milliliter levels. To bridge this gap, targeted liquid chromatography (LC) tandem MS (MS/MS) analysis of tryptic peptide surrogates using selected reaction monitoring detection has emerged as a viable option for rapid quantification of target proteins. The precision of this approach has been enhanced by the use of stable isotope-labeled peptide internal standards to compensate for variation in recovery and the influence of differential matrix effects. Unfortunately, the complexity of proteinaceous matrices, such as plasma, limits the usefulness of this approach to quantification in the mid-nanogram per milliliter range (medium-abundance proteins). This article reviews the current status of LC/MS/MS using selected reaction monitoring for protein quantification, and specifically considers the use of a single antibody to achieve superior enrichment of either the protein target or the released tryptic peptide. Examples of immunoaffinity-assisted LC/MS/MS are reviewed that demonstrate quantitative analysis of low-abundance proteins (subnanogram per milliliter range). A strategy based on this technology is proposed for the expedited evaluation of novel protein biomarkers, which relies on the synergy created from the complementary nature of MS and ELISA.
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Affiliation(s)
- Bradley L Ackermann
- Eli Lilly & Company, Drug Disposition, Greenfield Laboratories, Greenfield, IN 46140, USA.
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Abstract
Due to their versatility, quadrupole ion traps have become popular mass spectrometers in the growing field of proteomics. High sensitivity, user friendliness and low cost are the key features that have contributed to the success of the technology. However, mass measurement accuracy, resolution and mass range are still not comparable to the analytical performances obtained on other mass spectrometers. In the past 5 years, researchers have tried to overcome these drawbacks, focusing their attention on two different aspects of ion-trap mass spectrometry, development of novel types of ion traps and manipulation of the gas-phase ion chemistry, in order to obtain alternative techniques for tandem mass spectrometry analysis. In the field of trapping devices, improvements in instrumental design have led to the linear ion trap, digital ion trap and orbitrap. Activation methods based on electrons, chemically produced by an anion or from irradiation with an electron beam, have demonstrated their utility in providing complementary sequence information for improving confidence in protein identification.
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Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev Proteomics 2014; 3:611-9. [PMID: 17181475 DOI: 10.1586/14789450.3.6.611] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein profiling using mass spectrometry technology has emerged as a powerful method for analyzing large-scale protein-expression patterns in cells and tissues. However, a number of challenges are present in proteomics research, one of the greatest being the high degree of protein complexity and huge dynamic range of proteins expressed in the complex biological mixtures, which exceeds six orders of magnitude in cells and ten orders of magnitude in body fluids. Since many important signaling proteins have low expression levels, methods to detect the low-abundance proteins in a complex sample are required. This review will focus on the fundamental fractionation and mass spectrometry techniques currently used for large-scale shotgun proteomics research.
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Affiliation(s)
- Linfeng Wu
- University of Connecticut, School of Medicine, Department of Cell Biology, Farmington, Connecticut, CT 06030, USA.
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Mayya V, K Han D. Proteomic applications of protein quantification by isotope-dilution mass spectrometry. Expert Rev Proteomics 2014; 3:597-610. [PMID: 17181474 DOI: 10.1586/14789450.3.6.597] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the decades, isotope-dilution mass spectrometry (IDMS) has been implemented extensively for accurate quantification of drugs, metabolites and peptides in body fluids and tissues. More recently, it has been extended for quantifying specific proteins in complex mixtures. In this extended methodology, proteins are subjected to endoprotease action and specific resultant peptides are quantified by using synthetic stable isotope-labeled standard (SIS) peptides and IDMS. This article outlines the utilities and applications of quantifying proteins by IDMS, emphasizing its complementary value to global survey-based proteomic studies. The potential of SIS peptides to provide quantitative insights into cell signaling is also highlighted, with specific examples. Finally, we propose several novel mass spectrometric data acquisition strategies for large-scale applications of IDMS and SIS peptides in systems biology and protein biomarker validation studies.
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Affiliation(s)
- Viveka Mayya
- University of Connecticut Health Center, Department of Cell Biology and Center for Vascular Biology, Farmington, CT 06030, USA.
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