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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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2
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Vašíček J, Skiadopoulou D, Kuznetsova KG, Wen B, Johansson S, Njølstad PR, Bruckner S, Käll L, Vaudel M. Finding haplotypic signatures in proteins. Gigascience 2022; 12:giad093. [PMID: 37919975 PMCID: PMC10622322 DOI: 10.1093/gigascience/giad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/24/2023] [Accepted: 10/08/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can encode different amino acid sequences: protein haplotypes. These protein haplotypes are present in biological samples and detectable by mass spectrometry, but they are not accounted for in proteomic searches. Consequently, the impact of haplotypic variation on the results of proteomic searches and the discoverability of peptides specific to haplotypes remain unknown. FINDINGS Here, we study how common genetic haplotypes influence the proteomic search space and investigate the possibility to match peptides containing multiple amino acid substitutions to a publicly available data set of mass spectra. We found that for 12.42% of the discoverable amino acid substitutions encoded by common haplotypes, 2 or more substitutions may co-occur in the same peptide after tryptic digestion of the protein haplotypes. We identified 352 spectra that matched to such multivariant peptides, and out of the 4,582 amino acid substitutions identified, 6.37% were covered by multivariant peptides. However, the evaluation of the reliability of these matches remains challenging, suggesting that refined error rate estimation procedures are needed for such complex proteomic searches. CONCLUSIONS As these procedures become available and the ability to analyze protein haplotypes increases, we anticipate that proteomics will provide new information on the consequences of common variation, across tissues and time.
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Affiliation(s)
- Jakub Vašíček
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Dafni Skiadopoulou
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Ksenia G Kuznetsova
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Bo Wen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen 5021, Norway
| | - Stefan Bruckner
- Chair of Visual Analytics, Institute for Visual and Analytic Computing, University of Rostock, Rostock 18051, Germany
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH–Royal Institute of Technology, Solna 17121, Sweden
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo 0473, Norway
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3
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Kuznetsova KG, Levitsky LI, Pyatnitskiy MA, Ilina IY, Bubis JA, Solovyeva EM, Zgoda VG, Gorshkov MV, Moshkovskii SA. Cysteine alkylation methods in shotgun proteomics and their possible effects on methionine residues. J Proteomics 2020; 231:104022. [PMID: 33096305 DOI: 10.1016/j.jprot.2020.104022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/06/2020] [Accepted: 10/15/2020] [Indexed: 01/06/2023]
Abstract
In order to optimize sample preparation for shotgun proteomics, we compared four cysteine alkylating agents: iodoacetamide, chloroacetamide, 4-vinylpyridine and methyl methanethiosulfonate, and estimated their effects on the results of proteome analysis. Because alkylation may result in methionine modification in vitro, proteomics data were searched for methionine to isothreonine conversions, which may mimic genomic methionine to threonine substitutions found in proteogenomic analyses. We found that chloroacetamide was superior to the other reagents in terms of the number of identified peptides and undesirable off-site reactions. Among the reagents evaluated, iodoacetamide increased the rate of methionine-to-isothreonine conversion, especially if the sample was prepared in gel. The presence of proline following methionine in a protein sequence increased the modification rate as well. Generally, the methionine-to-isothreonine conversion events were relatively rare, but should be taken into account in proteogenomic studies when searching for single nucleotide polymorphism events at the protein level. Additionally, we have evaluated other methionine modifications, such as oxidation and carbamidomethylation. We found that carbamidomethylation may affect up to 80% of peptides containing methionine under the condition of iodoacetamide alkylation. In this case, carbamidomethylation of methionine is more common than oxidation and should be accounted for as a variable modification during proteomic search. SIGNIFICANCE: One of the most trending questions in bottom-up proteomics is the depth of proteome profiling, in other words, the coverage of proteins by identified tryptic peptides. In proteogenomics, where the identification of a single peptide, e.g. bearing an amino acid substitution, may be of interest, high sequence coverage is especially important. Chemical modifications during sample preparation may mimic biologically significant coding mutations at the proteome level. A typical example of such modification is methionine to isothreonine conversion during alkylation, which mimics methionine to threonine substitution in protein sequences due to respective genomic mutations. Therefore, the studies on the proper selection of alkylating reagents which balance the cysteine alkylation efficiency and the extent of methionine conversion upon conventional proteomic sample preparation workflow are crucial for the outcome of proteogenomic analyses and should present a general interest for the proteomic community.
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Affiliation(s)
- Ksenia G Kuznetsova
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.
| | - Lev I Levitsky
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 1, Leninsky Prospect, Moscow 119334, Russia
| | - Mikhail A Pyatnitskiy
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya, Moscow 119121, Russia
| | - Irina Y Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia
| | - Julia A Bubis
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 1, Leninsky Prospect, Moscow 119334, Russia
| | - Elizaveta M Solovyeva
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 1, Leninsky Prospect, Moscow 119334, Russia
| | - Victor G Zgoda
- Institute of Biomedical Chemistry, 10, Pogodinskaya, Moscow 119121, Russia; Skolkovo Institute of Science and Technology, 30, bld. 1, Bolshoy Boulevard, Moscow 121205, Russia
| | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 1, Leninsky Prospect, Moscow 119334, Russia
| | - Sergei A Moshkovskii
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova, Moscow 117997, Russia.
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4
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Kuznetsova KG, Solovyeva EM, Kuzikov AV, Gorshkov MV, Moshkovskii SA. [Modification of cysteine residues for mass spectrometry-based proteomic analysis: facts and artifacts]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:18-29. [PMID: 32116223 DOI: 10.18097/pbmc20206601018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mass spectrometric proteomic analysis at the sample preparation stage involves the artificial reduction of disulfide bonds in proteins formed between cysteine residues. Such bonds, when preserved in their native state, complicate subsequent enzymatic hydrolysis and interpretation of the research results. To prevent the re-formation of the disulfide bonds, cysteine residues are protected by special groups, most often by alkylation. In this review, we consider the methods used to modify cysteine residues during sample preparation, as well as possible artifacts of this stage. Particularly, adverse reactions of the alkylating agents with other amino acid residues are described. The most common alkylating compound used to protect cysteine residues in mass spectrometric proteomic analysis is iodoacetamide. However, an analysis of the literature in this area indicates that this reagent causes more adverse reactions than other agents used, such as chloroacetamide and acrylamide. The latter can be recommended for wider use. In the review we also discuss the features of the cysteine residue modifications and their influence on the efficiency of the search for post-translational modifications and protein products of single nucleotide substitutions.
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Affiliation(s)
| | - E M Solovyeva
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - A V Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - M V Gorshkov
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - S A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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5
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Levitsky LI, Kliuchnikova AA, Kuznetsova KG, Karpov DS, Ivanov MV, Pyatnitskiy MA, Kalinina OV, Gorshkov MV, Moshkovskii SA. Adenosine-to-Inosine RNA Editing in Mouse and Human Brain Proteomes. Proteomics 2019; 19:e1900195. [PMID: 31576663 DOI: 10.1002/pmic.201900195] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/25/2019] [Indexed: 12/30/2022]
Abstract
Proteogenomics is based on the use of customized genome or RNA sequencing databases for interrogation of shotgun proteomics data in search for proteome-level evidence of genome variations or RNA editing. In this work, the products of adenosine-to-inosine RNA editing in human and murine brain proteomes are identified using publicly available brain proteome LC-MS/MS datasets and an RNA editome database compiled from several sources. After filtering of false-positive results, 20 and 37 sites of editing in proteins belonging to 14 and 32 genes are identified for murine and human brain proteomes, respectively. Eight sites of editing identified with high spectral counts overlapped between human and mouse brain samples. Some of these sites have been previously reported using orthogonal methods, such as α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate receptors, CYFIP2, coatomer alpha. Also, differential editing between neurons and microglia is demonstrated in this work for some of the proteins from primary murine brain cell cultures. Because many edited sites are still not characterized functionally at the protein level, the results provide a necessary background for their further analysis in normal and diseased cells and tissues using targeted proteomic approaches.
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Affiliation(s)
- Lev I Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anna A Kliuchnikova
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow, 117997, Russia
| | - Ksenia G Kuznetsova
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia
| | - Dmitry S Karpov
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mikhail A Pyatnitskiy
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Onco Genotest LLC, Moscow, 125047, Russia.,Department of Technologies for Complex System Modelling, National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, 66123, Germany.,Medical Faculty, Saarland University, Kirrberger Straße, Homburg, 66421, Germany
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141700, Moscow Region, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow, 117997, Russia
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6
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Solovyeva EM, Kopysov VN, Pereverzev AY, Lobas AA, Moshkovskii SA, Gorshkov MV, Boyarkin OV. Method for Identification of Threonine Isoforms in Peptides by Ultraviolet Photofragmentation of Cold Ions. Anal Chem 2019; 91:6709-6715. [DOI: 10.1021/acs.analchem.9b00770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizaveta M. Solovyeva
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld.2 Moscow, 119334, Russia
| | - Vladimir N. Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Anna A. Lobas
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld.2 Moscow, 119334, Russia
| | | | - Mikhail V. Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld.2 Moscow, 119334, Russia
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
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7
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Kuznetsova KG, Ivanov MV, Pyatnitskiy MA, Levitsky LI, Ilina IY, Chernobrovkin AL, Zubarev RA, Gorhskov MV, Moshkovskii SA. Brain Proteome of Drosophila melanogaster Is Enriched with Nuclear Proteins. BIOCHEMISTRY (MOSCOW) 2019; 84:71-78. [PMID: 30927528 DOI: 10.1134/s0006297919010097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The brain proteome of Drosophila melanogaster was characterized by liquid chromatography/high-resolution mass spectrometry and compared to the earlier characterized Drosophila whole-body and head proteomes. Raw data for all the proteomes were processed in a similar manner. Approximately 4000 proteins were identified in the brain proteome that represented, as expected, the subsets of the head and body proteomes. However, after thorough data curation, we reliably identified 24 proteins unique for the brain proteome; 13 of them have never been detected before at the protein level. Fourteen of 24 identified proteins have been annotated as nuclear proteins. Comparison of three used datasets by label-free quantitation showed statistically significant enrichment of the brain proteome with nuclear proteins. Therefore, we recommend the use of isolated brain preparations in the studies of Drosophila nuclear proteins.
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Affiliation(s)
- K G Kuznetsova
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | - M V Ivanov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - M A Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.,Higher School of Economics, Moscow, 101000, Russia
| | - L I Levitsky
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - I Y Ilina
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | | | - R A Zubarev
- Karolinska Institutet, Stockholm, SE-171 77, Sweden.,Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - M V Gorhskov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - S A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, 119121, Russia. .,Pirogov Russian National Research Medical University (RNRMU), Moscow, 117997, Russia
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8
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Kuznetsova KG, Kliuchnikova AA, Ilina IU, Chernobrovkin AL, Novikova SE, Farafonova TE, Karpov DS, Ivanov MV, Goncharov AO, Ilgisonis EV, Voronko OE, Nasaev SS, Zgoda VG, Zubarev RA, Gorshkov MV, Moshkovskii SA. Proteogenomics of Adenosine-to-Inosine RNA Editing in the Fruit Fly. J Proteome Res 2018; 17:3889-3903. [DOI: 10.1021/acs.jproteome.8b00553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Anna A. Kliuchnikova
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | | | | | | | - Dmitry S. Karpov
- Institute of Biomedical Chemistry, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mark V. Ivanov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Anton O. Goncharov
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | | | - Shamsudin S. Nasaev
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | - Roman A. Zubarev
- Karolinska Institutet, Stockholm, Sweden
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Mikhail V. Gorshkov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Sergei A. Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
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9
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Moshkovskii SA, Ivanov MV, Kuznetsova KG, Gorshkov MV. Identification of Single Amino Acid Substitutions in Proteogenomics. BIOCHEMISTRY (MOSCOW) 2018; 83:250-258. [DOI: 10.1134/s0006297918030057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Ivanov MV, Lobas AA, Levitsky LI, Moshkovskii SA, Gorshkov MV. Brute-Force Approach for Mass Spectrometry-Based Variant Peptide Identification in Proteogenomics without Personalized Genomic Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:435-438. [PMID: 29299837 DOI: 10.1007/s13361-017-1859-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/05/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
In a proteogenomic approach based on tandem mass spectrometry analysis of proteolytic peptide mixtures, customized exome or RNA-seq databases are employed for identifying protein sequence variants. However, the problem of variant peptide identification without personalized genomic data is important for a variety of applications. Following the recent proposal by Chick et al. (Nat. Biotechnol. 33, 743-749, 2015) on the feasibility of such variant peptide search, we evaluated two available approaches based on the previously suggested "open" search and the "brute-force" strategy. To improve the efficiency of these approaches, we propose an algorithm for exclusion of false variant identifications from the search results involving analysis of modifications mimicking single amino acid substitutions. Also, we propose a de novo based scoring scheme for assessment of identified point mutations. In the scheme, the search engine analyzes y-type fragment ions in MS/MS spectra to confirm the location of the mutation in the variant peptide sequence. Graphical abstract ᅟ.
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Affiliation(s)
- Mark V Ivanov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141700, Russia
| | - Anna A Lobas
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141700, Russia
| | - Lev I Levitsky
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141700, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Mikhail V Gorshkov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141700, Russia.
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11
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Identification of Peptide AEDG in the Polypeptide Complex of the Pineal Gland. Bull Exp Biol Med 2017; 164:41-43. [PMID: 29124531 DOI: 10.1007/s10517-017-3922-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 10/18/2022]
Abstract
The polypeptide complex of the epiphysis and the peptide AEDG, constructed on the basis of its amino acid analysis, exert similar biological effects. Both bioregulators normalize melatonin synthesis in the pineal gland, functioning of the brain, eye retina, cardiovascular, endocrine, and immune systems; they also act as antioxidants, stress-protectors, and geroprotectors. Within the epiphysis polypeptide complex, free amino acids (3.26%), dipeptides (23.19%), tripeptides (50.72%), tetrapeptides (22.10%), and pentapeptides (0.72%) were revealed by mass spectrometry and HPLC. Peptide AEDG was detected among the tetrapeptides of the epiphysis polypeptide complex by selective reaction monitoring method. The biological effects of the epiphysis polypeptide complex are determined by the effect of its component AEDG.
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12
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Dimitrakopoulos L, Prassas I, Berns EMJJ, Foekens JA, Diamandis EP, Charames GS. Variant peptide detection utilizing mass spectrometry: laying the foundations for proteogenomic identification and validation. Clin Chem Lab Med 2017; 55:1291-1304. [PMID: 28157690 DOI: 10.1515/cclm-2016-0947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/07/2016] [Indexed: 01/29/2023]
Abstract
BACKGROUND Proteogenomics is an emerging field at the intersection of genomics and proteomics. Many variant peptides corresponding to single nucleotide variations (SNVs) are associated with specific diseases. The aim of this study was to demonstrate the feasibility of proteogenomic-based variant peptide detection in disease models and clinical specimens. METHODS We sought to detect p53 single amino acid variant (SAAV) peptides in breast cancer tumor samples that have been previously subjected to sequencing analysis. Initially, two cancer cell lines having a cellular tumor antigen p53 (TP53) mutation and one wild type for TP53 were analyzed by selected reaction monitoring (SRM) assays as controls. One pool of wild type and one pool of mutated for TP53 cytosolic extracts were assayed with a shotgun proteogenomic workflow. Furthermore, 18 individual samples having a mutation in TP53 were assayed by SRM. RESULTS Two mutant p53 peptides were successfully detected in two cancer cell lines as expected from their DNA sequence. Wild type p53 peptides were detected in both cytosolic pools, however, none of the mutant p53 peptides were identified. Mutations at the protein level were detected in two cytosolic extracts and whole tumor lysates from the same patients by SRM analysis. Six thousand and six hundred and twenty eight non-redundant proteins were identified in the two cytosolic pools, thus greatly improving a previously reported cytosolic proteome. CONCLUSIONS In the current study we show the great potential of using proteogenomics for the direct identification of cancer-associated mutations in clinical samples and we discuss current limitations and future perspectives.
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Hernandez-Valladares M, Vaudel M, Selheim F, Berven F, Bruserud Ø. Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers. Expert Rev Proteomics 2017; 14:649-663. [DOI: 10.1080/14789450.2017.1352474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Frode Selheim
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Berven
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
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Abstract
Omics approaches have become popular in biology as powerful discovery tools, and currently gain in interest for diagnostic applications. Establishing the accurate genome sequence of any organism is easy, but the outcome of its annotation by means of automatic pipelines remains imprecise. Some protein-encoding genes may be missed as soon as they are specific and poorly conserved in a given taxon, while important to explain the specific traits of the organism. Translational starts are also poorly predicted in a relatively important number of cases, thus impacting the protein sequence database used in proteomics, comparative genomics, and systems biology. The use of high-throughput proteomics data to improve genome annotation is an attractive option to obtain a more comprehensive molecular picture of a given organism. Here, protocols for reannotating prokaryote genomes are described based on shotgun proteomics and derivatization of protein N-termini with a positively charged reagent coupled to high-resolution tandem mass spectrometry.
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Lobas AA, Karpov DS, Kopylov AT, Solovyeva EM, Ivanov MV, Ilina IY, Lazarev VN, Kuznetsova KG, Ilgisonis EV, Zgoda VG, Gorshkov MV, Moshkovskii SA. Exome-based proteogenomics of HEK-293 human cell line: Coding genomic variants identified at the level of shotgun proteome. Proteomics 2016; 16:1980-91. [DOI: 10.1002/pmic.201500349] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 03/30/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Anna A. Lobas
- Institute of Biomedical Chemistry; Moscow Russia
- Institute for Energy Problems of Chemical Physics; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Dolgoprudny Moscow Region Russia
| | - Dmitry S. Karpov
- Institute of Biomedical Chemistry; Moscow Russia
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow Russia
| | | | - Elizaveta M. Solovyeva
- Institute for Energy Problems of Chemical Physics; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Dolgoprudny Moscow Region Russia
| | - Mark V. Ivanov
- Institute for Energy Problems of Chemical Physics; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Dolgoprudny Moscow Region Russia
| | | | - Vassily N. Lazarev
- Research Institute of Physico-Chemical Medicine; Federal Medical and Biological Agency; Moscow Russia
| | | | | | | | - Mikhail V. Gorshkov
- Institute for Energy Problems of Chemical Physics; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Dolgoprudny Moscow Region Russia
| | - Sergei A. Moshkovskii
- Institute of Biomedical Chemistry; Moscow Russia
- Medico-Biological Faculty; Pirogov Russian National Research Medical University (RNRMU); Moscow Russia
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16
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Kuznetsova KG, Trufanov PV, Moysa AA, Pyatnitskiy MA, Zgoda VG, Gorshkov MV, Moshkovskii SA. Threonine versus isothreonine in synthetic peptides analyzed by high-resolution liquid chromatography/tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1323-1331. [PMID: 27173114 DOI: 10.1002/rcm.7566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE One of the problems in proteogenomic research aimed at identification of variant peptides is the presence of peptides with amino acid isomers of different origin in the analyzed samples. Among the most challenging examples are peptides with threonine and isothreonine (homoserine) in their sequences. Indeed, the latter residue may appear in vitro as a methionine substitution during sample preparation for shotgun proteome analysis. Yet, this substitution of Met to isoThr is not encoded genetically and should be unambiguously distinguished from, e.g., point mutations in proteins that result in Met conversion to Thr. METHODS In this work we compared tandem mass (MS/MS) spectra produced by an Orbitrap mass spectrometer of Thr- and isoThr-containing tryptic peptides and found a distinctive feature in their collisionally activated fragmentation patterns. RESULTS Up to 84% of MS/MS spectra for peptides containing isoThr residues have been positively specified. We also studied the differences in retention times for peptides containing Thr isoforms that can be further used for their distinction. CONCLUSIONS Threonine can be distinguished from isothreonine by its retention time and HCD fragmentation pattern, specifically relative intensity of the bn - product ion, which can be further used in proteomic research. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Pavel V Trufanov
- Institute of Biomedical Chemistry, Moscow, Russia
- Moscow State University, Biological Faculty, Moscow, Russia
| | - Alexander A Moysa
- Institute of Biomedical Chemistry, Moscow, Russia
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Mikhail V Gorshkov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Medical University, Moscow, Russia
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17
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Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:521-45. [PMID: 27049631 PMCID: PMC4991544 DOI: 10.1146/annurev-anchem-071015-041722] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.
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Affiliation(s)
- Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706;
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18
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Kliuchnikova A, Kuznetsova K, Moshkovskii S. ADAR-mediated messenger RNA editing: analysis at the proteome level. ACTA ACUST UNITED AC 2016; 62:510-519. [DOI: 10.18097/pbmc20166205510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Post-transcriptional RNA editing by RNA specific adenosine deaminases (ADAR) was discovered more than two decades ago. It provides additional regulation of animal and human transcriptome. In most cases, it occurs in nervous tissue, where, as a result of the reaction, adenosine is converted to inosine in particular sites of RNA. In case of messenger RNA, during translation, inosine is recognized as guanine leading to amino acid substitutions. Those substitutions are shown to affect substantially the function of proteins, e.g. subunits of the glutamate receptor. Nevertheless, most of the works on RNA editing use analysis of nucleic acids, even those which deal with a coding RNA. In this review, we propose the use of shotgun proteomics based on high resolution liquid chromatography and mass spectrometry for investigation of the effects of RNA editing at the protein level. Recently developed methods of big data processing allow combining the results of various omics techniques, being referred to as proteogenomics. The proposed proteogenomic approach for the analysis of RNA editing at the protein level will directly conduct a qualitative and quantitative analysis of protein edited sequences in the scale of whole proteome.
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Affiliation(s)
| | | | - S.A. Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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19
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Kumar D, Mondal AK, Kutum R, Dash D. Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes. Proteomics 2015; 16:226-40. [PMID: 26773550 DOI: 10.1002/pmic.201500263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/18/2015] [Accepted: 09/28/2015] [Indexed: 01/04/2023]
Abstract
Sustainable innovations in sequencing technologies have resulted in a torrent of microbial genome sequencing projects. However, the prokaryotic genomes sequenced so far are unequally distributed along their phylogenetic tree; few phyla contain the majority, the rest only a few representatives. Accurate genome annotation lags far behind genome sequencing. While automated computational prediction, aided by comparative genomics, remains a popular choice for genome annotation, substantial fraction of these annotations are erroneous. Proteogenomics utilizes protein level experimental observations to annotate protein coding genes on a genome wide scale. Benefits of proteogenomics include discovery and correction of gene annotations regardless of their phylogenetic conservation. This not only allows detection of common, conserved proteins but also the discovery of protein products of rare genes that may be horizontally transferred or taxonomy specific. Chances of encountering such genes are more in rare phyla that comprise a small number of complete genome sequences. We collated all bacterial and archaeal proteogenomic studies carried out to date and reviewed them in the context of genome sequencing projects. Here, we present a comprehensive list of microbial proteogenomic studies, their taxonomic distribution, and also urge for targeted proteogenomics of underexplored taxa to build an extensive reference of protein coding genes.
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Affiliation(s)
- Dhirendra Kumar
- G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India
| | - Anupam Kumar Mondal
- G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India
| | - Rintu Kutum
- G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India
| | - Debasis Dash
- G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India
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20
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Polyakova A, Kuznetsova K, Moshkovskii S. Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens. Expert Rev Proteomics 2015; 12:533-41. [DOI: 10.1586/14789450.2015.1070100] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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