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Kuril AK. Exploring the versatility of mass spectrometry: Applications across diverse scientific disciplines. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2024:14690667241278110. [PMID: 39314187 DOI: 10.1177/14690667241278110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Mass spectrometry (MS) has become a pivotal analytical tool across various scientific disciplines due to its ability to provide detailed molecular information with high sensitivity and specificity. MS plays a crucial role in various fields, including drug discovery and development, proteomics, metabolomics, environmental analysis, and clinical diagnostics and Forensic science. In this article we are discussing the application of MS across the diverse scientific disciplines by focusing on some classical examples from each field of application. As the technology continues to evolve, it promises to unlock new possibilities in scientific research and practical applications, cementing its position as an essential tool in modern analytical science.
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Lee JW, Chen EY, Hu T, Perret R, Chaffee ME, Martinov T, Mureli S, McCurdy CL, Jones LA, Gafken PR, Chanana P, Su Y, Chapuis AG, Bradley P, Schmitt TM, Greenberg PD. Overcoming immune evasion from post-translational modification of a mutant KRAS epitope to achieve TCR-engineered T cell-mediated antitumor activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.612965. [PMID: 39345486 PMCID: PMC11429761 DOI: 10.1101/2024.09.18.612965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
T cell receptor (TCR)-T cell immunotherapy, in which T cells are engineered to express a TCR specific for a tumor epitope, is a form of adoptive cell therapy (ACT) that has demonstrated promise against various tumor types. Mutants of oncoprotein KRAS, particularly at glycine-12 (G12), are frequent drivers of tumorigenicity, but also attractive targets for TCR-T cell therapy. However, MHC class I-restricted TCRs specifically targeting G12-mutant KRAS epitopes in the context of tumors expressing HLA-A2, the most common human HLA-A allele, have remained elusive despite evidence that an epitope encompassing the mutation can bind HLA-A2 and induce T cell responses. We report that post-translational modifications of the protein on this epitope may allow tumor cells to evade immunologic pressure from TCR-T cells. A lysine side chain-methylated KRAS G12V peptide, rather than unmodified epitope, may be presented in HLA-A2 by tumor cells and impact recognition by TCRs. Using a novel computationally guided approach to design TCRs, we developed by mutagenesis TCRs that recognize this methylated peptide, enhancing tumor recognition and destruction. Additionally, we identified TCRs with similar functional activity in normal repertoires from rare primary T cells by stimulation with modified peptide, clonal expansion, and selection. Mechanistically, a gene knockout screen to identify mechanism(s) by which tumor cells methylate or demethylate this epitope unveiled SPT6 as a demethylating protein that could be targeted to improve effectiveness of these TCRs. These findings highlight the role of post-translational modifications in immune evasion and suggest that identifying and targeting such modifications should facilitate development of more effective TCR-T cell therapies.
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Cai Y. Conjugation of primary amine groups in targeted proteomics. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39229771 DOI: 10.1002/mas.21906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/21/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
Primary amines, in the form of unmodified N-terminus of peptide/protein and unmodified lysine residue, are perhaps the most important functional groups that can serve as the starting points in proteomic analysis, especially via mass spectrometry-based approaches. A variety of multifunctional probes that conjugate primary amine groups through covalent bonds have been developed and employed to facilitate protein/protein complex characterization, including identification, quantification, structure and localization elucidation, protein-protein interaction investigation, and so forth. As an integral part of more accurate peptide quantification in targeted proteomics, isobaric stable isotope-coded primary amine labeling approaches eventually facilitated protein/peptide characterization at the single-cell level, paving the way for single-cell proteomics. The development and advances in the field can be reviewed in terms of key components of a multifunctional probe: functional groups and chemistry for primary amine conjugation; hetero-bifunctional moiety for separation/enrichment of conjugated protein/protein complex; and functionalized linker/spacer. Perspectives are primarily focused on optimizing primary amine conjugation under physiological conditions to improve characterization of native proteins, especially those associated with the surface of living cells/microorganisms.
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Affiliation(s)
- Yang Cai
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA
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4
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Hamzelou S, Belobrajdic D, Broadbent JA, Juhász A, Lee Chang K, Jameson I, Ralph P, Colgrave ML. Utilizing proteomics to identify and optimize microalgae strains for high-quality dietary protein: a review. Crit Rev Biotechnol 2023:1-16. [PMID: 38035669 DOI: 10.1080/07388551.2023.2283376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Algae-derived protein has immense potential to provide high-quality protein foods for the expanding human population. To meet its potential, a broad range of scientific tools are required to identify optimal algal strains from the hundreds of thousands available and identify ideal growing conditions for strains that produce high-quality protein with functional benefits. A research pipeline that includes proteomics can provide a deeper interpretation of microalgal composition and biochemistry in the pursuit of these goals. To date, proteomic investigations have largely focused on pathways that involve lipid production in selected microalgae species. Herein, we report the current state of microalgal proteome measurement and discuss promising approaches for the development of protein-containing food products derived from algae.
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Affiliation(s)
| | | | | | - Angéla Juhász
- School of Science, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, Joondalup, Australia
| | | | - Ian Jameson
- CSIRO Ocean and Atmosphere, Hobart, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, St Lucia, Australia
- School of Science, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, Joondalup, Australia
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Cvekl A, Camerino MJ. Generation of Lens Progenitor Cells and Lentoid Bodies from Pluripotent Stem Cells: Novel Tools for Human Lens Development and Ocular Disease Etiology. Cells 2022; 11:3516. [PMID: 36359912 PMCID: PMC9658148 DOI: 10.3390/cells11213516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In vitro differentiation of human pluripotent stem cells (hPSCs) into specialized tissues and organs represents a powerful approach to gain insight into those cellular and molecular mechanisms regulating human development. Although normal embryonic eye development is a complex process, generation of ocular organoids and specific ocular tissues from pluripotent stem cells has provided invaluable insights into the formation of lineage-committed progenitor cell populations, signal transduction pathways, and self-organization principles. This review provides a comprehensive summary of recent advances in generation of adenohypophyseal, olfactory, and lens placodes, lens progenitor cells and three-dimensional (3D) primitive lenses, "lentoid bodies", and "micro-lenses". These cells are produced alone or "community-grown" with other ocular tissues. Lentoid bodies/micro-lenses generated from human patients carrying mutations in crystallin genes demonstrate proof-of-principle that these cells are suitable for mechanistic studies of cataractogenesis. Taken together, current and emerging advanced in vitro differentiation methods pave the road to understand molecular mechanisms of cataract formation caused by the entire spectrum of mutations in DNA-binding regulatory genes, such as PAX6, SOX2, FOXE3, MAF, PITX3, and HSF4, individual crystallins, and other genes such as BFSP1, BFSP2, EPHA2, GJA3, GJA8, LIM2, MIP, and TDRD7 represented in human cataract patients.
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Affiliation(s)
- Aleš Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael John Camerino
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Zhang W, Yang C, Liu J, Liang Z, Shan Y, Zhang L, Zhang Y. Accurate discrimination of leucine and isoleucine residues by combining continuous digestion with multiple MS 3 spectra integration in protein sequence. Talanta 2022; 249:123666. [PMID: 35717752 DOI: 10.1016/j.talanta.2022.123666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/26/2022]
Abstract
Protein de novo sequencing based on tandem mass spectrometry is a crucial technology that enables the identification of peptides without searching databases and assembling unknown sequence proteins, especially for monoclonal antibodies (mAbs). However, the discrimination of leucine (Leu) and isoleucine (Ile) residues in the target protein sequence is still challenging. Herein, we developed an accurate method by continuous digestion with MS3-based fragmentation and multiple spectra integration (evaluated by combined verification score, CVS) to distinguish Leu and Ile residues. Continuous digestion promotes the diversity of peptides in order to expose more Leu and Ile at the N-terminal. CVS integrates multiple MS3 spectra to reduce the interference from noise and co-fragmented ions and improve accuracy. This method successfully resolved all 75 Leu/Ile in bovine serum albumin, especially 3 consecutive Leu/Ile. We further applied the method to analyze trastuzumab and 67 out of the 68 Leu/Ile from the light chain and heavy chain were accurately discriminated, demonstrating the great potential in mAbs sequencing.
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Affiliation(s)
- Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chao Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
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Suomi T, Elo LL. Statistical and machine learning methods to study human CD4+ T cell proteome profiles. Immunol Lett 2022; 245:8-17. [DOI: 10.1016/j.imlet.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/05/2022]
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Pan N, Wang Z, Wang B, Wan J, Wan C. Mapping Microproteins and ncRNA-Encoded Polypeptides in Different Mouse Tissues. Front Cell Dev Biol 2021; 9:687748. [PMID: 34381774 PMCID: PMC8350139 DOI: 10.3389/fcell.2021.687748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/30/2021] [Indexed: 12/30/2022] Open
Abstract
Small open reading frame encoded peptides (SEPs), also called microproteins, play a vital role in biological processes. Plenty of their open reading frames are located within the non-coding RNA (ncRNA) range. Recent research has demonstrated that ncRNA-encoded polypeptides have essential functions and exist ubiquitously in various tissues. To better understand the role of microproteins, especially ncRNA-encoded proteins, expressed in different tissues, we profiled the proteomic characterization of five mouse tissues by mass spectrometry, including bottom-up, top-down, and de novo sequencing strategies. Bottom-up and top-down with database-dependent searches identified 811 microproteins in the OpenProt database. De novo sequencing identified 290 microproteins, including 12 ncRNA-encoded microproteins that were not found in current databases. In this study, we discovered 1,074 microproteins in total, including 270 ncRNA-encoded microproteins. From the annotation of these microproteins, we found that the brain contains the largest number of neuropeptides, while the spleen contains the most immunoassociated microproteins. This suggests that microproteins in different tissues have tissue-specific functions. These unannotated ncRNA-coded microproteins have predicted domains, such as the macrophage migration inhibitory factor domain and the Prefoldin domain. These results expand the mouse proteome and provide insight into the molecular biology of mouse tissues.
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Affiliation(s)
- Ni Pan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhiwei Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Bing Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Jian Wan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Cuihong Wan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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Vitorino R, Guedes S, Trindade F, Correia I, Moura G, Carvalho P, Santos MAS, Amado F. De novo sequencing of proteins by mass spectrometry. Expert Rev Proteomics 2020; 17:595-607. [PMID: 33016158 DOI: 10.1080/14789450.2020.1831387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed. AREAS COVERED De novo protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for de novo sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data. EXPERT OPINION As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, de-novo protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification.
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Affiliation(s)
- Rui Vitorino
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal.,iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal.,Unidade De Investigação Cardiovascular, Departamento De Cirurgia E Fisiologia, Faculdade De Medicina, Universidade Do Porto , Porto, Portugal
| | - Sofia Guedes
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal
| | - Fabio Trindade
- Unidade De Investigação Cardiovascular, Departamento De Cirurgia E Fisiologia, Faculdade De Medicina, Universidade Do Porto , Porto, Portugal
| | - Inês Correia
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Gabriela Moura
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Paulo Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, FIOCRUZ, Laboratory for Proteomics and Protein Engineering , Brazil
| | - Manuel A S Santos
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Francisco Amado
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal
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10
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Dos Santos-Silva CA, Zupin L, Oliveira-Lima M, Vilela LMB, Bezerra-Neto JP, Ferreira-Neto JR, Ferreira JDC, de Oliveira-Silva RL, Pires CDJ, Aburjaile FF, de Oliveira MF, Kido EA, Crovella S, Benko-Iseppon AM. Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era. Bioinform Biol Insights 2020; 14:1177932220952739. [PMID: 32952397 PMCID: PMC7476358 DOI: 10.1177/1177932220952739] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.
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Affiliation(s)
| | - Luisa Zupin
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy
| | - Marx Oliveira-Lima
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - José Diogo Cavalcanti Ferreira
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil.,Departamento de Genética, Instituto Federal de Pernambuco, Pesqueira, Brazil
| | | | | | | | | | - Ederson Akio Kido
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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Veras MA, Lim YJ, Kuljanin M, Lajoie GA, Urquhart BL, Séguin CA. Protocol for parallel proteomic and metabolomic analysis of mouse intervertebral disc tissues. JOR Spine 2020; 3:e1099. [PMID: 33015574 PMCID: PMC7524214 DOI: 10.1002/jsp2.1099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/25/2020] [Accepted: 05/14/2020] [Indexed: 01/07/2023] Open
Abstract
The comprehensiveness of data collected by "omics" modalities has demonstrated the ability to drastically transform our understanding of the molecular mechanisms of chronic, complex diseases such as musculoskeletal pathologies, how biomarkers are identified, and how therapeutic targets are developed. Standardization of protocols will enable comparisons between findings reported by multiple research groups and move the application of these technologies forward. Herein, we describe a protocol for parallel proteomic and metabolomic analysis of mouse intervertebral disc (IVD) tissues, building from the combined expertise of our collaborative team. This protocol covers dissection of murine IVD tissues, sample isolation, and data analysis for both proteomics and metabolomics applications. The protocol presented below was optimized to maximize the utility of a mouse model for "omics" applications, accounting for the challenges associated with the small starting quantity of sample due to small tissue size as well as the extracellular matrix-rich nature of the tissue.
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Affiliation(s)
- Matthew A Veras
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry The University of Western Ontario London Ontario Canada
- Bone and Joint Institute The University of Western Ontario London Ontario Canada
| | - Yong J Lim
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry The University of Western Ontario London Ontario Canada
| | - Miljan Kuljanin
- Department of Cell Biology Harvard Medical School Boston Massachusetts USA
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry The University of Western Ontario London Ontario Canada
| | - Bradley L Urquhart
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry The University of Western Ontario London Ontario Canada
| | - Cheryle A Séguin
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry The University of Western Ontario London Ontario Canada
- Bone and Joint Institute The University of Western Ontario London Ontario Canada
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Cautereels J, Van Hee N, Chatterjee S, Van Alsenoy C, Lemière F, Blockhuys F. QCMS 2 as a new method for providing insight into peptide fragmentation: The influence of the side-chain and inter-side-chain interactions. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4446. [PMID: 31652378 DOI: 10.1002/jms.4446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/12/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
The identification of peptides and proteins from tandem mass spectra is a difficult task and multiple tools have been developed to aid this identification. We present a new method called quantum chemical mass spectrometry for materials science (QCMS2 ), which is based on quantum chemical calculations of bond orders, reaction, and transition-state energies at the DFT/B3LYP/6-311+G* level of theory. The method was used to describe the fragmentation pathways of five X-His-Ser tripeptides with X = Asn, Asp, Glu, Ser, and Trp, thereby focusing on the influence of the side chain and inter-side-chain interactions on the fragmentation. The main features in the mass spectra of the five tripeptides were correctly reproduced, and a number of fragments were assigned to fragmentations involving the side chain and the influence of inter-side-chain interactions. Product ion spectra were recorded to evaluate the capabilities and limitations of QCMS2 and a number of conventional tools.
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Affiliation(s)
- Julie Cautereels
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Nils Van Hee
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Sneha Chatterjee
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | | | - Filip Lemière
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Frank Blockhuys
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
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13
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Cautereels J, Giribaldi J, Enjalbal C, Blockhuys F. Quantum chemical mass spectrometry: Ab initio study of b 2 -ion formation mechanisms for the singly protonated Gln-His-Ser tripeptide. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8778. [PMID: 32144813 DOI: 10.1002/rcm.8778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Both amide bond protonation triggering peptide fragmentations and the controversial b2 -ion structures have been subjects of intense research. The involvement of histidine (H), with its imidazole side chain that induces specific dissociation patterns involving inter-side-chain (ISC) interactions, in b2 -ion formation was investigated, focusing on the QHS model tripeptide. METHODS To identify the effect of histidine on fragmentations issued from ISC interactions, QHS was selected for a comprehensive analysis of the pathways leading to the three possible b2 -ion structures, using quantum chemical calculations performed at the DFT/B3LYP/6-311+G* level of theory. Electrospray ionization ion trap mass spectrometry allowed the recording of MS2 and MS3 tandem mass spectra, whereas the Quantum Chemical Mass Spectrometry for Materials Science (QCMS2 ) method was used to predict fragmentation patterns. RESULTS Whereas it is very difficult to differentiate among protonated oxazolone, diketopiperazine, or lactam b2 -ions using MS2 and MS3 mass spectra, the calculations indicated that the QH b2 -ion (detected at m/z 266) is probably a mixture of the lactam and oxazolone structures formed after amide nitrogen protonation, making the formation of diketopiperazine less likely as it requires an additional step for its formation. CONCLUSIONS In contrast to glycine-histidine-containing b2 -ions, known to be issued from the backbone-imidazole cyclization, we found that interactions between the side chains were not obvious to perceive, neither from a thermodynamics nor from a fragmentation perspective, emphasizing the importance of the whole sequence on the dissociation behavior usually demonstrated from simple glycine-containing tripeptides.
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Affiliation(s)
- Julie Cautereels
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | | | | | - Frank Blockhuys
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
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14
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Shiferaw GA, Vandermarliere E, Hulstaert N, Gabriels R, Martens L, Volders PJ. COSS: A Fast and User-Friendly Tool for Spectral Library Searching. J Proteome Res 2020; 19:2786-2793. [PMID: 32384242 DOI: 10.1021/acs.jproteome.9b00743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Spectral similarity searching to identify peptide-derived MS/MS spectra is a promising technique, and different spectrum similarity search tools have therefore been developed. Each of these tools, however, comes with some limitations, mainly because of low processing speed and issues with handling large databases. Furthermore, the number of spectral data formats supported is typically limited, which also creates a threshold to adoption. We have therefore developed COSS (CompOmics Spectral Searching), a new and user-friendly spectral library search tool supporting two scoring functions. COSS also includes decoy spectra generation for result validation. We have benchmarked COSS on three different spectral libraries and compared the results with established spectral searching tools and a sequence database search tool. Our comparison showed that COSS more reliably identifies spectra, is capable of handling large data sets and libraries, and is an easy to use tool that can run on low computer specifications. COSS binaries and source code can be freely downloaded from https://github.com/compomics/COSS.
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Affiliation(s)
- Genet Abay Shiferaw
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Elien Vandermarliere
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Niels Hulstaert
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Pieter-Jan Volders
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, 9000 Ghent, Belgium
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15
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Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
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Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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16
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17
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Abstract
Mounting evidence implicates hybrid insulin peptides (HIPs) as important autoantigens in the development of type 1 diabetes (T1D). These fusion peptides formed between insulin and other pancreatic beta cell-derived peptides contain non-genomically encoded amino acid sequences, making them plausible targets for autoreactive T cells in T1D. HIPs are detectable by mass spectrometry in human and murine islets and are targeted by diabetes-inducing T cells in non-obese diabetic mice as well as by T cells isolated from the residual pancreatic islets of human organ donors with T1D. The discovery of HIPs comes with numerous new challenges, as well as opportunities to study the pathogenesis of T1D. Here we review the original discovery of HIPs and describe recent studies investigating the role of HIP-reactive T cells in the development of diabetes. We also discuss potential mechanisms that may be responsible for the generation of HIPs in beta cells and describe challenges that need to be addressed in the field of mass spectrometry to enable the discovery of new HIPs. The identification of these potentially disease-driving antigens in T1D is of key interest to the field as it may provide new tools to predict, prevent and potentially reverse the disease.
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Affiliation(s)
- T A Wiles
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz, Aurora, CO, USA
| | - T Delong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz, Aurora, CO, USA
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18
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Abstract
The mechanism underlying many biological phenotypes remains unknown despite the increasing availability of whole genome and transcriptome sequencing. Direct measurement of changes in protein expression is an attractive alternative and has the potential to reveal novel processes. Mass spectrometry has become the standard method for proteomics, allowing both the confident identification and quantification of thousands of proteins from biological samples. In this review, mass spectrometry-based proteomic methods and their applications are described.
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Affiliation(s)
- J Robert O'Neill
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK. Robert.o'.,Department of Clinical Surgery, Royal Infirmary of Edinburgh, Edinburgh, UK. Robert.o'
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19
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Frank Y, Hruz T, Tschager T, Venzin V. Improved de novo peptide sequencing using LC retention time information. Algorithms Mol Biol 2018; 13:14. [PMID: 30181767 PMCID: PMC6114869 DOI: 10.1186/s13015-018-0132-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/20/2018] [Indexed: 12/03/2022] Open
Abstract
Background Liquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides that elute one after another are analyzed via tandem mass spectrometry by measuring the mass-to-charge ratio of a peptide and its fragments. De novo peptide sequencing is the problem of reconstructing the amino acid sequences of a peptide from this measurement data. Past de novo sequencing algorithms solely consider the mass spectrum of the fragments for reconstructing a sequence. Results We propose to additionally exploit the information obtained from liquid chromatography. We study the problem of computing a sequence that is not only in accordance with the experimental mass spectrum, but also with the chromatographic retention time. We consider three models for predicting the retention time and develop algorithms for de novo sequencing for each model. Conclusions Based on an evaluation for two prediction models on experimental data from synthesized peptides we conclude that the identification rates are improved by exploiting the chromatographic information. In our evaluation, we compare our algorithms using the retention time information with algorithms using the same scoring model, but not the retention time.
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20
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Volkova PY, Geras'kin SA. 'Omic' technologies as a helpful tool in radioecological research. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 189:156-167. [PMID: 29677564 DOI: 10.1016/j.jenvrad.2018.04.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.
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Affiliation(s)
- Polina Yu Volkova
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia.
| | - Stanislav A Geras'kin
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia
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21
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Barbieri R, Guryev V, Brandsma CA, Suits F, Bischoff R, Horvatovich P. Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 926:21-47. [PMID: 27686804 DOI: 10.1007/978-3-319-42316-6_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Proteogenomics is a multi-omics research field that has the aim to efficiently integrate genomics, transcriptomics and proteomics. With this approach it is possible to identify new patient-specific proteoforms that may have implications in disease development, specifically in cancer. Understanding the impact of a large number of mutations detected at the genomics level is needed to assess the effects at the proteome level. Proteogenomics data integration would help in identifying molecular changes that are persistent across multiple molecular layers and enable better interpretation of molecular mechanisms of disease, such as the causal relationship between single nucleotide polymorphisms (SNPs) and the expression of transcripts and translation of proteins compared to mainstream proteomics approaches. Identifying patient-specific protein forms and getting a better picture of molecular mechanisms of disease opens the avenue for precision and personalized medicine. Proteogenomics is, however, a challenging interdisciplinary science that requires the understanding of sample preparation, data acquisition and processing for genomics, transcriptomics and proteomics. This chapter aims to guide the reader through the technology and bioinformatics aspects of these multi-omics approaches, illustrated with proteogenomics applications having clinical or biological relevance.
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Affiliation(s)
- Ruggero Barbieri
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology & Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Frank Suits
- IBM T.J. Watson Research Centre, 1101 Kitchawan Road, Yorktown Heights, New York, 10598, NY, USA
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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22
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Dong Z, Kennedy E, Hokmabadi M, Timp G. Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore. ACS NANO 2017; 11:5440-5452. [PMID: 28538092 DOI: 10.1021/acsnano.6b08452] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
It is now possible to create, in a thin inorganic membrane, a single, sub-nanometer-diameter pore (i.e., a sub-nanopore) about the size of an amino acid residue. To explore the prospects for sequencing protein with it, measurements of the force and current were performed as two denatured histones, which differed by four amino acid residue substitutions, were impelled systematically through the sub-nanopore one at a time using an atomic force microscope. The force measurements revealed that once the denatured protein, stabilized by sodium dodecyl sulfate (SDS), translocated through the sub-nanopore, a disproportionately large force was required to pull it back. This was interpreted to mean that the SDS was cleaved from the protein during the translocation. The force measurements also exposed a dichotomy in the translocation kinetics: either the molecule slid nearly frictionlessly through the pore or it slipped-and-stuck. When it slid frictionlessly, regardless of whether the molecule was pulled N-terminus or C-terminus first through the pore, regular patterns were observed intermittently in the force and blockade current fluctuations that corresponded to the distance between stretched residues. Furthermore, the amplitude of the fluctuations in the current blockade were correlated with the occluded volume associated with the amino acid residues in the pore. Finally, a comparison of the patterns in the current fluctuations associated with the two practically identical histones supported the conclusion that a sub-nanopore was sensitive enough to discriminate amino acid substitutions in the sequence of a single protein molecule by measuring volumes of 0.1 nm3 per read.
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Affiliation(s)
- Zhuxin Dong
- Department of Electrical Engineering and ‡Departments of Electrical Engineering and Biological Science, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Eamonn Kennedy
- Department of Electrical Engineering and ‡Departments of Electrical Engineering and Biological Science, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Mohammad Hokmabadi
- Department of Electrical Engineering and ‡Departments of Electrical Engineering and Biological Science, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Gregory Timp
- Department of Electrical Engineering and ‡Departments of Electrical Engineering and Biological Science, University of Notre Dame , Notre Dame, Indiana 46556, United States
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23
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Kuchibhotla B, Kola SR, Medicherla JV, Cherukuvada SV, Dhople VM, Nalam MR. Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1216-1226. [PMID: 28349438 DOI: 10.1007/s13361-017-1606-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/30/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. Graphical Abstract ᅟ.
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Affiliation(s)
- Bhanuramanand Kuchibhotla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Sankara Rao Kola
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Jagannadham V Medicherla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Swamy V Cherukuvada
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Vishnu M Dhople
- Department of Functional Genomics, University Medicine Greifswald, Interface Institute Genetics & Functional Genomics, D-17475, Greifswald, Germany
| | - Madhusudhana Rao Nalam
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
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24
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Tschager T, Rösch S, Gillet L, Widmayer P. A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses. Algorithms Mol Biol 2017; 12:12. [PMID: 28603547 PMCID: PMC5464308 DOI: 10.1186/s13015-017-0104-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/19/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Given a peptide as a string of amino acids, the masses of all its prefixes and suffixes can be found by a trivial linear scan through the amino acid masses. The inverse problem is the idealde novopeptide sequencing problem: Given all prefix and suffix masses, determine the string of amino acids. In biological reality, the given masses are measured in a lab experiment, and measurements by necessity are noisy. The (real, noisy) de novo peptide sequencing problem therefore has a noisy input: a few of the prefix and suffix masses of the peptide are missing and a few other masses are given in addition. For this setting, we ask for an amino acid string that explains the given masses as accurately as possible. RESULTS Past approaches interpreted accuracy by searching for a string that explains as many masses as possible. We feel, however, that it is not only bad to not explain a mass that appears, but also to explain a mass that does not appear. We propose to minimize the symmetric difference between the set of given masses and the set of masses that the string explains. For this new optimization problem, we propose an efficient algorithm that computes both the best and the k best solutions. Proof-of-concept experiments on measurements of synthesized peptides show that our approach leads to better results compared to finding a string that explains as many given masses as possible. CONCLUSIONS We conclude that considering the symmetric difference as optimization goal can improve the identification rates for de novo peptide sequencing. A preliminary version of this work has been presented at WABI 2016.
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25
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Keiblinger KM, Fuchs S, Zechmeister-Boltenstern S, Riedel K. Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. FEMS Microbiol Ecol 2016; 92:fiw180. [PMID: 27549116 PMCID: PMC5026301 DOI: 10.1093/femsec/fiw180] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 08/18/2016] [Indexed: 11/14/2022] Open
Abstract
The increasing application of soil metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies. In addition, we present recent applications of soil metaproteomics and discuss how such approaches, linking phylogenetics and functionality, can help gain deeper insights into terrestrial microbial ecology. Finally, we strongly recommend that to maximize the insights environmental metaproteomics may provide, such methods should be employed within a holistic experimental approach considering relevant aboveground and belowground ecosystem parameters.
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Affiliation(s)
- Katharina M Keiblinger
- Institute for Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Strasse 82, 1190 Vienna, Austria
| | - Stephan Fuchs
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17489 Greifswald, Germany
| | - Sophie Zechmeister-Boltenstern
- Institute for Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Strasse 82, 1190 Vienna, Austria
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17489 Greifswald, Germany
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26
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Díez P, Fuentes M. Proteogenomics for the Comprehensive Analysis of Human Cellular and Serum Antibody Repertoires. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:153-162. [PMID: 27686811 DOI: 10.1007/978-3-319-42316-6_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The vast repertoire of immunoglobulins produced by the immune system is a consequence of the huge amount of antigens to which we are exposed every day. The diversity of these immunoglobulins is due to different mechanisms (including VDJ recombination, somatic hypermutation, and antigen selection). Understanding how the immune system is capable of generating this diversity and which are the molecular bases of the composition of immunoglobulins are key challenges in the immunological field. During the last decades, several techniques have emerged as promising strategies to achieve these goals, but it is their combination which appears to be the fruitful solution for increasing the knowledge about human cellular and serum antibody repertoires.In this chapter, we address the diverse strategies focused on the analysis of immunoglobulin repertoires as well as the characterization of the genomic and peptide sequences. Moreover, the advantages of combining various -omics approaches are discussed through review different published studies, showing the benefits in clinical areas.
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain. .,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain.
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27
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Refsgaard JC, Munk S, Jensen LJ. Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics. Methods Mol Biol 2016; 1355:323-39. [PMID: 26584936 DOI: 10.1007/978-1-4939-3049-4_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Advances in mass spectrometric instrumentation in the past 15 years have resulted in an explosion in the raw data yield from typical phosphoproteomics workflows. This poses the challenge of confidently identifying peptide sequences, localizing phosphosites to proteins and quantifying these from the vast amounts of raw data. This task is tackled by computational tools implementing algorithms that match the experimental data to databases, providing the user with lists for downstream analysis. Several platforms for such automated interpretation of mass spectrometric data have been developed, each having strengths and weaknesses that must be considered for the individual needs. These are reviewed in this chapter. Equally critical for generating highly confident output datasets is the application of sound statistical criteria to limit the inclusion of incorrect peptide identifications from database searches. Additionally, careful filtering and use of appropriate statistical tests on the output datasets affects the quality of all downstream analyses and interpretation of the data. Our considerations and general practices on these aspects of phosphoproteomics data processing are presented here.
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Affiliation(s)
- Jan C Refsgaard
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Bldg. 6.2, 2200, Copenhagen, Denmark.,Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Bldg. 6.2, 2200, Copenhagen, Denmark
| | - Stephanie Munk
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Bldg. 6.2, 2200, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Bldg. 6.2, 2200, Copenhagen, Denmark.
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28
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Giese SH, Zickmann F, Renard BY. Detection of Unknown Amino Acid Substitutions Using Error-Tolerant Database Search. Methods Mol Biol 2016; 1362:247-264. [PMID: 26519182 DOI: 10.1007/978-1-4939-3106-4_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent studies have demonstrated that mass spectrometry-based variant detection is feasible. Typically, either genomic variant databases or transcript data are used to construct customized target databases for the identification of single-amino acid variants in mass spectrometry data. However, both approaches require additional data to perform the identification of SAAVs. Here, we discuss the application of an error-tolerant peptide search engine such as BICEPS for identifying variants exclusively based on standard Uniprot databases. Thereby, unnecessary and redundant extensions of the search space are avoided. The workflow provides an unbiased view on the data; the search space is not limited to known variants and simultaneously does not require additional data. In a subsequent step a second identification search is performed to verify the initially identified variant peptides and aggregate information on the protein level.
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Affiliation(s)
- Sven H Giese
- Research Group Bioinformatics (NG4), Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany
- Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Franziska Zickmann
- Research Group Bioinformatics (NG4), Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG4), Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany.
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29
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Large-scale label-free phosphoproteomics: from technology to data interpretation. Bioanalysis 2015; 6:2403-20. [PMID: 25384593 DOI: 10.4155/bio.14.188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein phosphorylation plays a central role in the dynamic intracellular signaling and the control of biochemical pathways in all living cells. Recent advances in high-performance MS/MS-based technology make the large-scale identification and quantification of phosphorylation sites possible. Here, we review the full data generation pipeline, starting from sample preparation methods and LC-MS detection procedures, through to data processing and analysis software tools that facilitate the systematic comparative profiling of thousands of phosphoproteins in different biological specimens in a single experiment. We emphasize current challenges and promising avenues for the mechanistic interpretation and visualization of global phosphorylation networks and their relevance to human health and disease.
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30
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Methionine to isothreonine conversion as a source of false discovery identifications of genetically encoded variants in proteogenomics. J Proteomics 2015; 120:169-78. [DOI: 10.1016/j.jprot.2015.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 03/03/2015] [Accepted: 03/07/2015] [Indexed: 01/07/2023]
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31
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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32
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Sanggaard KW, Dyrlund TF, Thomsen LR, Nielsen TA, Brøndum L, Wang T, Thøgersen IB, Enghild JJ. Characterization of the gila monster (Heloderma suspectum suspectum) venom proteome. J Proteomics 2015; 117:1-11. [DOI: 10.1016/j.jprot.2015.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/06/2015] [Accepted: 01/10/2015] [Indexed: 12/23/2022]
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33
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Lin SY, Hsu WH, Lin CC, Chen CJ. Mass spectrometry-based proteomics in Chest Medicine, Gerontology, and Nephrology: subgroups omics for personalized medicine. Biomedicine (Taipei) 2014; 4:25. [PMID: 25520938 PMCID: PMC4264973 DOI: 10.7603/s40681-014-0025-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/30/2014] [Indexed: 12/12/2022] Open
Abstract
Mass spectrometry (MS) is currently the most promising tool for studying proteomics to investigate largescale proteins in a specific proteome. Emerging MS-based proteomics is widely applied to decipher complex proteome for discovering potential biomarkers. Given its growing usage in clinical medicine for biomarker discovery to predict, diagnose and confer prognosis, MS-based proteomics can benefit study of personalized medicine. In this review we introduce some fundamental MS theory and MS-based quantitative proteomic approaches as well as several representative clinical MS-based proteomics issues in Chest Medicine, Gerontology, and Nephrology.
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Affiliation(s)
- Shih-Yi Lin
- Institute of Clinical Medical Science, China Medical University College of Medicine, 404 Taichung, Taiwan
- Department of Internal Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- Division of Nephrology and Kidney Institute, China Medical University Hospital, 404 Taichung, Taiwan
| | - Wu-Huei Hsu
- Institute of Clinical Medical Science, China Medical University College of Medicine, 404 Taichung, Taiwan
- Department of Internal Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- Division of Pulmonary and Critical Care Medicine, China Medical University Hospital and China Medical University, 404 Taichung, Taiwan
| | - Cheng-Chieh Lin
- Institute of Clinical Medical Science, China Medical University College of Medicine, 404 Taichung, Taiwan
- Department of Family Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- School of Medicine, College of Medicine China Medical University, No. 91, Hsueh Shih Road, 404 Taichung, Taiwan
| | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, No. 91, Hsueh-Shih Road, 402 Taichung, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, 404 Taichung, Taiwan
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Aguilar-Pontes MV, de Vries RP, Zhou M. (Post-)genomics approaches in fungal research. Brief Funct Genomics 2014; 13:424-39. [PMID: 25037051 DOI: 10.1093/bfgp/elu028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functional studies beyond genomes are required. Thanks to the developments of current -omics techniques, it is possible to produce large amounts of fungal functional data in a high-throughput fashion (e.g. transcriptome, proteome, etc.). The increasing ease of creating -omics data has also created a major challenge for downstream data handling and analysis. Numerous databases, tools and software have been created to meet this challenge. Facing such a richness of techniques and information, hereby we provide a brief roadmap on current wet-lab and bioinformatics approaches to study functional genomics in fungi.
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Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA. Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:63-76. [PMID: 23467006 PMCID: PMC3898926 DOI: 10.1016/j.bbapap.2013.02.032] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 02/05/2013] [Accepted: 02/22/2013] [Indexed: 12/23/2022]
Abstract
Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
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Affiliation(s)
- Yasset Perez-Riverol
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba
| | - Rui Wang
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Markus Müller
- Proteome Informatics Group, Swiss Institute of Bioinformatics, CMU - 1, rue Michel Servet CH-1211 Geneva, Switzerland
| | - Vladimir Vesada
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba
| | - Juan Antonio Vizcaíno
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Verheggen K, Barsnes H, Martens L. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics 2013; 14:367-77. [PMID: 24285552 DOI: 10.1002/pmic.201300288] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/09/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022]
Abstract
Modern day proteomics generates ever more complex data, causing the requirements on the storage and processing of such data to outgrow the capacity of most desktop computers. To cope with the increased computational demands, distributed architectures have gained substantial popularity in the recent years. In this review, we provide an overview of the current techniques for distributed computing, along with examples of how the techniques are currently being employed in the field of proteomics. We thus underline the benefits of distributed computing in proteomics, while also pointing out the potential issues and pitfalls involved.
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Affiliation(s)
- Kenneth Verheggen
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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37
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Ibáñez C, Simó C, García-Cañas V, Cifuentes A, Castro-Puyana M. Metabolomics, peptidomics and proteomics applications of capillary electrophoresis-mass spectrometry in Foodomics: A review. Anal Chim Acta 2013; 802:1-13. [DOI: 10.1016/j.aca.2013.07.042] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/20/2013] [Accepted: 07/17/2013] [Indexed: 01/05/2023]
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38
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Bruce C, Stone K, Gulcicek E, Williams K. Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies. ACTA ACUST UNITED AC 2013; Chapter 13:13.21.1-13.21.17. [PMID: 23504934 DOI: 10.1002/0471250953.bi1321s41] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mass spectrometry has become a major tool in the study of proteomes. The analysis of proteolytic peptides and their fragment ions by this technique enables the identification and quantitation of the precursor proteins in a mixture. However, deducing chemical structures and then protein sequences from mass-to-charge ratios is a challenging computational task. Software tools incorporating powerful algorithms and statistical methods improved our ability to process the large quantities of proteomics data. Repositories of spectral data make both data analysis and experimental design more efficient. New approaches in quantitative and statistical proteomics make possible a greater coverage of the proteome, the identification of more post-translational modifications, and a greater sensitivity in the quantitation of targeted proteins.
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Affiliation(s)
- Can Bruce
- W.M. Keck Foundation Biotechnology Resource Laboratory and Molecular Biochemistry and Biophysics Department, Yale University, New Haven, Connecticut, USA
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39
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Strum JS, Nwosu CC, Hua S, Kronewitter SR, Seipert RR, Bachelor RJ, An HJ, Lebrilla CB. Automated assignments of N- and O-site specific glycosylation with extensive glycan heterogeneity of glycoprotein mixtures. Anal Chem 2013; 85:5666-75. [PMID: 23662732 DOI: 10.1021/ac4006556] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Site-specific glycosylation (SSG) of glycoproteins remains a considerable challenge and limits further progress in the areas of proteomics and glycomics. Effective methods require new approaches in sample preparation, detection, and data analysis. While the field has advanced in sample preparation and detection, automated data analysis remains an important goal. A new bioinformatics approach implemented in software called GP Finder automatically distinguishes correct assignments from random matches and complements experimental techniques that are optimal for glycopeptides, including nonspecific proteolysis and high mass resolution liquid chromatography/tandem mass spectrometry (LC/MS/MS). SSG for multiple N- and O-glycosylation sites, including extensive glycan heterogeneity, was annotated for single proteins and protein mixtures with a 5% false-discovery rate, generating hundreds of nonrandom glycopeptide matches and demonstrating the proof-of-concept for a self-consistency scoring algorithm shown to be compliant with the target-decoy approach (TDA). The approach was further applied to a mixture of N-glycoproteins from unprocessed human milk and O-glycoproteins from very-low-density-lipoprotein (vLDL) particles.
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Affiliation(s)
- John S Strum
- Department of Chemistry, University of California, Davis, California 95616, USA
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40
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Faccin M, Bruscolini P. MS/MS Spectra Interpretation as a Statistical–Mechanics Problem. Anal Chem 2013; 85:4884-92. [DOI: 10.1021/ac4005666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mauro Faccin
- Departamento de Física
Teórica &
Instituto de Biocomputacíon y Física de Sistemas Complejos
(BIFI), Universidad de Zaragoza, c/Mariano
Esquillors s/n, 50018 Zaragoza, Spain
| | - Pierpaolo Bruscolini
- Departamento de Física
Teórica &
Instituto de Biocomputacíon y Física de Sistemas Complejos
(BIFI), Universidad de Zaragoza, c/Mariano
Esquillors s/n, 50018 Zaragoza, Spain
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41
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Horvatić A, Dodig I, Vuletić T, Pavoković D, Hameršak Z, Butorac A, Cindrić M. Comparison between Enhanced MALDI In-source Decay by Ammonium Persulfate and N- or C-Terminal Derivatization Methods for Detailed Peptide Structure Determination. Anal Chem 2013; 85:3940-7. [DOI: 10.1021/ac303436n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anita Horvatić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Ivana Dodig
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | | | | | - Zdenko Hameršak
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | | | - Mario Cindrić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
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42
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Champagne A, Boutry M. Proteomics of nonmodel plant species. Proteomics 2013; 13:663-73. [PMID: 23125178 DOI: 10.1002/pmic.201200312] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 01/10/2023]
Abstract
Until recently, large scale proteomic investigations in the plant field have only been possible for a few model species for which the whole genome sequence had been fully determined. In contrast, for many other species with a strong economic interest as sources of human food and animal feed, as well as industrial and pharmacological molecules, little was known about their genome sequence and identifying the proteome in these species was still considered challenging. However, progress has been made as a result of several recent advances in proteomics tools, e.g. in MS technology and data search programs, and the increasing availability of genomic and cDNA sequences from various species. Moreover, next-generation sequencing technologies now make it possible to rapidly determine, at a reasonable cost, the genome or RNA sequence of species not currently considered as models, thus considerably expanding the plant sequence databases. This review will show how these advances make it possible to identify a large set of proteins, even for species for which few sequences are currently available.
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Affiliation(s)
- Antoine Champagne
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, Louvain-la-Neuve, Belgium
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Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL. The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res 2012; 12:162-71. [PMID: 23215161 DOI: 10.1021/pr301012j] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Human Proteome Project was launched in September 2010 with the goal of characterizing at least one protein product from each protein-coding gene. Here we assess how much of the proteome has been detected to date via tandem mass spectrometry by analyzing PeptideAtlas, a compendium of human derived LC-MS/MS proteomics data from many laboratories around the world. All data sets are processed with a consistent set of parameters using the Trans-Proteomic Pipeline and subjected to a 1% protein FDR filter before inclusion in PeptideAtlas. Therefore, PeptideAtlas contains only high confidence protein identifications. To increase proteome coverage, we explored new comprehensive public data sources for data likely to add new proteins to the Human PeptideAtlas. We then folded these data into a Human PeptideAtlas 2012 build and mapped it to Swiss-Prot, a protein sequence database curated to contain one entry per human protein coding gene. We find that this latest PeptideAtlas build includes at least one peptide for each of ~12500 Swiss-Prot entries, leaving ~7500 gene products yet to be confidently cataloged. We characterize these "PA-unseen" proteins in terms of tissue localization, transcript abundance, and Gene Ontology enrichment, and propose reasons for their absence from PeptideAtlas and strategies for detecting them in the future.
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Affiliation(s)
- Terry Farrah
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
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44
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A support for the identification of non-tryptic peptides based on low resolution tandem and sequential mass spectrometry data: The INSPIRE software. Anal Chim Acta 2012; 718:70-7. [DOI: 10.1016/j.aca.2012.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 12/28/2011] [Accepted: 01/02/2012] [Indexed: 11/17/2022]
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45
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Darville LNF, Merchant ME, Maccha V, Siddavarapu VR, Hasan A, Murray KK. Isolation and determination of the primary structure of a lectin protein from the serum of the American alligator (Alligator mississippiensis). Comp Biochem Physiol B Biochem Mol Biol 2011; 161:161-9. [PMID: 22085437 DOI: 10.1016/j.cbpb.2011.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 10/15/2022]
Abstract
Mass spectrometry in conjunction with de novo sequencing was used to determine the amino acid sequence of a 35kDa lectin protein isolated from the serum of the American alligator that exhibits binding to mannose. The protein N-terminal sequence was determined using Edman degradation and enzymatic digestion with different proteases was used to generate peptide fragments for analysis by liquid chromatography tandem mass spectrometry (LC MS/MS). Separate analysis of the protein digests with multiple enzymes enhanced the protein sequence coverage. De novo sequencing was accomplished using MASCOT Distiller and PEAKS software and the sequences were searched against the NCBI database using MASCOT and BLAST to identify homologous peptides. MS analysis of the intact protein indicated that it is present primarily as monomer and dimer in vitro. The isolated 35kDa protein was ~98% sequenced and found to have 313 amino acids and nine cysteine residues and was identified as an alligator lectin. The alligator lectin sequence was aligned with other lectin sequences using DIALIGN and ClustalW software and was found to exhibit 58% and 59% similarity to both human and mouse intelectin-1. The alligator lectin exhibited strong binding affinities toward mannan and mannose as compared to other tested carbohydrates.
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Affiliation(s)
- Lancia N F Darville
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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46
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Chang KY, Muddiman DC. Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms. BMC Genomics 2011; 12:358. [PMID: 21745387 PMCID: PMC3146456 DOI: 10.1186/1471-2164-12-358] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 07/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Database searching is the most frequently used approach for automated peptide assignment and protein inference of tandem mass spectra. The results, however, depend on the sequences in target databases and on search algorithms. Recently by using an alternative splicing database, we identified more proteins than with the annotated proteins in Aspergillus flavus. In this study, we aimed at finding a greater number of eligible splice variants based on newly available transcript sequences and the latest genome annotation. The improved database was then used to compare four search algorithms: Mascot, OMSSA, X! Tandem, and InsPecT. RESULTS The updated alternative splicing database predicted 15833 putative protein variants, 61% more than the previous results. There was transcript evidence for 50% of the updated genes compared to the previous 35% coverage. Database searches were conducted using the same set of spectral data, search parameters, and protein database but with different algorithms. The false discovery rates of the peptide-spectrum matches were estimated < 2%. The numbers of the total identified proteins varied from 765 to 867 between algorithms. Whereas 42% (1651/3891) of peptide assignments were unanimous, the comparison showed that 51% (568/1114) of the RefSeq proteins and 15% (11/72) of the putative splice variants were inferred by all algorithms. 12 plausible isoforms were discovered by focusing on the consensus peptides which were detected by at least three different algorithms. The analysis found different conserved domains in two putative isoforms of UDP-galactose 4-epimerase. CONCLUSIONS We were able to detect dozens of new peptides using the improved alternative splicing database with the recently updated annotation of the A. flavus genome. Unlike the identifications of the peptides and the RefSeq proteins, large variations existed between the putative splice variants identified by different algorithms. 12 candidates of putative isoforms were reported based on the consensus peptide-spectrum matches. This suggests that applications of multiple search engines effectively reduced the possible false positive results and validated the protein identifications from tandem mass spectra using an alternative splicing database.
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Affiliation(s)
- Kung-Yen Chang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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47
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Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC–MS for biomarker discovery. Talanta 2011; 83:1209-24. [DOI: 10.1016/j.talanta.2010.10.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 10/18/2010] [Accepted: 10/21/2010] [Indexed: 01/30/2023]
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48
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An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences. PLoS One 2010; 5:e13968. [PMID: 21103051 PMCID: PMC2980473 DOI: 10.1371/journal.pone.0013968] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 08/24/2010] [Indexed: 01/08/2023] Open
Abstract
Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300-500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide synthesis and cofactor biosynthesis, allowing classification of bacteria by observation of conserved processes. Additionally, within these core functionalities, we observed proteins involved in the alternative lactate utilization pathway, recently described in Shewanella.
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49
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Ma B. Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 2010; 25:107-123. [DOI: 10.1007/s11390-010-9309-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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