1
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Mansuri MS, Bathla S, Lam TT, Nairn AC, Williams KR. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. J Proteomics 2024; 297:105109. [PMID: 38325732 PMCID: PMC10939724 DOI: 10.1016/j.jprot.2024.105109] [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: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
To identify proteins by the bottom-up mass spectrometry workflow, enzymatic digestion is essential to break down proteins into smaller peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity and generation of peptides with desirable positively charged N- and C-terminal amino acid residues that are amenable to reverse phase HPLC separation and MS/MS analyses. However, trypsin can yield variable digestion profiles and its protein cleavage activity is interdependent on trypsin source and quality, digestion time and temperature, pH, denaturant, trypsin and substrate concentrations, composition/complexity of the sample matrix, and other factors. There is therefore a need for a more standardized, general-purpose trypsin digestion protocol. Based on a review of the literature we delineate optimal conditions for carrying out trypsin digestions of complex proteomes from bulk samples to limiting amounts of protein extracts. Furthermore, we highlight recent developments and technological advances used in digestion protocols to quantify complex proteomes from single cells. SIGNIFICANCE: Currently, bottom-up MS-based proteomics is the method of choice for global proteome analysis. Since trypsin is the most utilized protease in bottom-up MS proteomics, delineating optimal conditions for carrying out trypsin digestions of complex proteomes in samples ranging from tissues to single cells should positively impact a broad range of biomedical research.
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Affiliation(s)
- M Shahid Mansuri
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA.
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2
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Hoare M, Tan R, Welle KA, Swovick K, Hryhorenko JR, Ghaemmaghami S. Methionine Alkylation as an Approach to Quantify Methionine Oxidation Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:433-440. [PMID: 38324783 PMCID: PMC10921467 DOI: 10.1021/jasms.3c00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Post-translational oxidation of methionine residues can destabilize proteins or modify their functions. Although levels of methionine oxidation can provide important information regarding the structural integrity and regulation of proteins, their quantitation is often challenging as analytical procedures in and of themselves can artifactually oxidize methionines. Here, we develop a mass-spectrometry-based method called Methionine Oxidation by Blocking with Alkylation (MObBa) that quantifies methionine oxidation by selectively alkylating and blocking unoxidized methionines. Thus, alkylated methionines can be used as a stable proxy for unoxidized methionines. Using proof of concept experiments, we demonstrate that MObBa can be used to measure methionine oxidation levels within individual synthetic peptides and on proteome-wide scales. MObBa may provide a straightforward experimental strategy for mass spectrometric quantitation of methionine oxidation.
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Affiliation(s)
- Margaret Hoare
- Department
of Biology, University of Rochester, Rochester, New York 14627, United States
| | - Ruiyue Tan
- Department
of Biology, University of Rochester, Rochester, New York 14627, United States
| | - Kevin A. Welle
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
| | - Kyle Swovick
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
| | - Jennifer R. Hryhorenko
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
| | - Sina Ghaemmaghami
- Department
of Biology, University of Rochester, Rochester, New York 14627, United States
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
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3
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Moltó E, Pintado C, Louzada RA, Bernal-Mizrachi E, Andrés A, Gallardo N, Bonzon-Kulichenko E. Unbiased Phosphoproteome Mining Reveals New Functional Sites of Metabolite-Derived PTMs Involved in MASLD Development. Int J Mol Sci 2023; 24:16172. [PMID: 38003361 PMCID: PMC10671570 DOI: 10.3390/ijms242216172] [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: 09/12/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are paramount in health and disease. Phosphoproteome analysis by enrichment techniques is becoming increasingly attractive for biomedical research. Recent findings show co-enrichment of other phosphate-containing biologically relevant PTMs, but these results were obtained by closed searches focused on the modifications sought. Open searches are a breakthrough in high-throughput PTM analysis (OS-PTM), identifying practically all PTMs detectable by mass spectrometry, even unknown ones, with their modified sites, in a hypothesis-free and deep manner. Here we reanalyze liver phosphoproteome by OS-PTM, demonstrating its extremely complex nature. We found extensive Lys glycerophosphorylations (pgK), as well as modification with glycerylphosphorylethanolamine on Glu (gpetE) and flavin mononucleotide on His (fmnH). The functionality of these metabolite-derived PTMs is demonstrated during metabolic dysfunction-associated steatotic liver disease (MASLD) development in mice. MASLD elicits specific alterations in pgK, epgE and fmnH in the liver, mainly on glycolytic enzymes and mitochondrial proteins, suggesting an increase in glycolysis and mitochondrial ATP production from the early insulin-resistant stages. Thus, we show new possible mechanisms based on metabolite-derived PTMs leading to intrahepatic lipid accumulation during MASLD development and reinforce phosphoproteome enrichment as a valuable tool with which to study the functional implications of a variety of low-abundant phosphate-containing PTMs in cell physiology.
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Affiliation(s)
- Eduardo Moltó
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain
| | - Cristina Pintado
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain
| | - Ruy Andrade Louzada
- Department of Internal Medicine, Division of Endocrinology, Diabetes and Metabolism, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ernesto Bernal-Mizrachi
- Department of Internal Medicine, Division of Endocrinology, Diabetes and Metabolism, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Antonio Andrés
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain
| | - Nilda Gallardo
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain
| | - Elena Bonzon-Kulichenko
- Biochemistry Section, Regional Center for Biomedical Research (CRIB), Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain
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4
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Pavek JG, Frey BL, Frost DC, Gu TJ, Li L, Smith LM. Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue. Anal Chem 2023; 95:15245-15253. [PMID: 37791746 PMCID: PMC10637319 DOI: 10.1021/acs.analchem.3c02473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Top-down proteomics, the tandem mass spectrometric analysis of intact proteoforms, is the dominant method for proteoform characterization in complex mixtures. While this strategy produces detailed molecular information, it also requires extensive instrument time per mass spectrum obtained and thus compromises the depth of proteoform coverage that is accessible on liquid chromatography time scales. Such a top-down analysis is necessary for making original proteoform identifications, but once a proteoform has been confidently identified, the extensive characterization it provides may no longer be required for a subsequent identification of the same proteoform. We present a strategy to identify proteoforms in tissue samples on the basis of the combination of an intact mass determination with a measured count of the number of cysteine residues present in each proteoform. We developed and characterized a cysteine tagging chemistry suitable for the efficient and specific labeling of cysteine residues within intact proteoforms and for providing a count of the cysteine amino acids present. On simple protein mixtures, the tagging chemistry yields greater than 98% labeling of all cysteine residues, with a labeling specificity of greater than 95%. Similar results are observed on more complex samples. In a proof-of-principle study, proteoforms present in a human prostate tumor biopsy were characterized. Observed proteoforms, each characterized by an intact mass and a cysteine count, were grouped into proteoform families (groups of proteoforms originating from the same gene). We observed 2190 unique experimental proteoforms, 703 of which were grouped into 275 proteoform families.
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Affiliation(s)
- John G. Pavek
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706
| | - Brian L. Frey
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706
| | - Dustin C. Frost
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705
| | - Ting-Jia Gu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706
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Nickerson JL, Doucette AA. Maximizing Cumulative Trypsin Activity with Calcium at Elevated Temperature for Enhanced Bottom-Up Proteome Analysis. BIOLOGY 2022; 11:biology11101444. [PMID: 36290348 PMCID: PMC9598648 DOI: 10.3390/biology11101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Simple Summary Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is time consuming though still may yield poor digestion efficiency. While raising the temperature should theoretically accelerate the digestion, it also destabilizes the enzyme and promotes trypsin de-activation. We therefore questioned whether elevated temperature is beneficial for improving tryptic digestion. Here, we quantify protein digestion kinetics at elevated temperatures for calcium-stabilized trypsin and enforce the critical importance of calcium ions to preserve the enzyme. We quantitatively demonstrate that 1 h at 47 °C provides a superior digest when compared to conventional (overnight, 37 °C) processing of the proteome. The practical impact of our enhanced digestion protocol is shown through bottom-up mass spectrometry analysis of a complex proteome mixture. Abstract Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency.
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6
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A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications. J Proteomics 2022; 261:104576. [DOI: 10.1016/j.jprot.2022.104576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/20/2022]
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7
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Savić ND, Salazar Marcano DE, Parac-Vogt TN. Expanding the Scope of Polyoxometalates as Artificial Proteases towards Hydrolysis of Insoluble Proteins. Chemistry 2021; 28:e202104224. [PMID: 34860460 DOI: 10.1002/chem.202104224] [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: 11/25/2021] [Indexed: 11/08/2022]
Abstract
Despite the enormous importance of insoluble proteins in biological processes, their structural investigation remains a challenging task. The development of artificial enzyme-like catalysts would greatly facilitate the elucidation of their structure since currently used enzymes in proteomics largely lose activity in the presence of surfactants, which are necessary to solubilize insoluble proteins. In this study, the hydrolysis of a fully insoluble protein by polyoxometalate complexes as artificial proteases in surfactant solutions is reported for the first time. The hydrolysis of zein as a model protein was investigated in the presence of Zr(IV) and Hf(IV) substituted Keggin-type polyoxometalates (POMs), (Et2 NH2 )10 [M(α-PW11 O39 )2 ] (M = Zr or Hf), and different concentrations of the anionic surfactant sodium dodecyl sulfate (SDS). Selective hydrolysis of the protein upon incubation with the catalyst was observed, and the results indicate that the hydrolytic selectivity and activity of the POM catalysts strongly depends on the concentration of surfactant. The molecular interactions between the POM catalyst and zein in the presence of SDS were explored using a combination of spectroscopic techniques which indicated competitive binding between POM and SDS towards the protein. Furthermore, the formation of micellar superstructures in ternary POM/surfactant/protein solutions has been confirmed by conductivity and Dynamic Light Scattering measurements.
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Affiliation(s)
- Nada D Savić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
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8
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Espinosa LA, Ramos Y, Andújar I, Torres EO, Cabrera G, Martín A, Roche D, Chinea G, Becquet M, González I, Canaán-Haden C, Nelson E, Rojas G, Pérez-Massón B, Pérez-Martínez D, Boggiano T, Palacio J, Lozada Chang SL, Hernández L, de la Luz Hernández KR, Markku S, Vitikainen M, Valdés-Balbín Y, Santana-Medero D, Rivera DG, Vérez-Bencomo V, Emalfarb M, Tchelet R, Guillén G, Limonta M, Pimentel E, Ayala M, Besada V, González LJ. In-solution buffer-free digestion allows full-sequence coverage and complete characterization of post-translational modifications of the receptor-binding domain of SARS-CoV-2 in a single ESI-MS spectrum. Anal Bioanal Chem 2021; 413:7559-7585. [PMID: 34739558 PMCID: PMC8569510 DOI: 10.1007/s00216-021-03721-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/04/2022]
Abstract
Subunit vaccines based on the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 provide one of the most promising strategies to fight the COVID-19 pandemic. The detailed characterization of the protein primary structure by mass spectrometry (MS) is mandatory, as described in ICHQ6B guidelines. In this work, several recombinant RBD proteins produced in five expression systems were characterized using a non-conventional protocol known as in-solution buffer-free digestion (BFD). In a single ESI-MS spectrum, BFD allowed very high sequence coverage (≥ 99%) and the detection of highly hydrophilic regions, including very short and hydrophilic peptides (2-8 amino acids), and the His6-tagged C-terminal peptide carrying several post-translational modifications at Cys538 such as cysteinylation, homocysteinylation, glutathionylation, truncated glutathionylation, and cyanylation, among others. The analysis using the conventional digestion protocol allowed lower sequence coverage (80-90%) and did not detect peptides carrying most of the above-mentioned PTMs. The two C-terminal peptides of a dimer [RBD(319-541)-(His)6]2 linked by an intermolecular disulfide bond (Cys538-Cys538) with twelve histidine residues were only detected by BFD. This protocol allows the detection of the four disulfide bonds present in the native RBD, low-abundance scrambling variants, free cysteine residues, O-glycoforms, and incomplete processing of the N-terminal end, if present. Artifacts generated by the in-solution BFD protocol were also characterized. BFD can be easily implemented; it has been applied to the characterization of the active pharmaceutical ingredient of two RBD-based vaccines, and we foresee that it can be also helpful to the characterization of mutated RBDs.
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Affiliation(s)
- Luis Ariel Espinosa
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Yassel Ramos
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Ivan Andújar
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Enso Onill Torres
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Gleysin Cabrera
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Alejandro Martín
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Diamilé Roche
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Glay Chinea
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Mónica Becquet
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Isabel González
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Camila Canaán-Haden
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Elías Nelson
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Gertrudis Rojas
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | | | - Tamy Boggiano
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | - Julio Palacio
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | - Lourdes Hernández
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | - Saloheimo Markku
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | - Marika Vitikainen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | | | | | - Daniel G Rivera
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana, Zapata & G, 10400, Havana, Cuba
| | | | - Mark Emalfarb
- Dyadic International, Inc, 140 Intercoastal Pointe Drive, Suite #404, Jupiter, FL, 33477, USA
| | - Ronen Tchelet
- Dyadic International, Inc, 140 Intercoastal Pointe Drive, Suite #404, Jupiter, FL, 33477, USA
| | - Gerardo Guillén
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Miladys Limonta
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Eulogio Pimentel
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Marta Ayala
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Vladimir Besada
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Luis Javier González
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba.
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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10
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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11
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Levitsky LI, Bubis JA, Gorshkov MV, Tarasova IA. AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results. J Proteomics 2021; 248:104350. [PMID: 34389500 DOI: 10.1016/j.jprot.2021.104350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/21/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022]
Abstract
Characterization of post-translational modifications is among the most challenging tasks in tandem mass spectrometry-based proteomics which has yet to find an efficient solution. The ultra-tolerant (open) database search attempts to meet this challenge. However, interpretation of the mass shifts observed in open search still requires an effective and automated solution. We have previously introduced the AA_stat tool for analysis of amino acid frequencies at different mass shifts and generation of hypotheses on unaccounted in vitro modifications. Here, we report on the new version of AA_stat, which now complements amino acid frequency statistics with a number of new features: (1) MS/MS-based localization of mass shifts and localization scoring, including shifts which are the sum of modifications; (2) inferring fixed modifications to increase method sensitivity; (3) inferring monoisotopic peak assignment errors and variable modifications based on abundant mass shift localizations to increase the yield of closed search; (4) new mass calibration algorithm to account for partial systematic shifts; (5) interactive integration of all results and a rated list of possible mass shift interpretations. With these options, we improve interpretation of open search results and demonstrate the utility of AA_stat for profiling of abundant and rare amino acid modifications. AA_stat is implemented in Python as an open-source command-line tool available at https://github.com/SimpleNumber/aa_stat. SIGNIFICANCE: Mass spectrometry-based PTM characterization has a long history, yet most of the methods rely on a priori knowledge of modifications of interest and do not provide a whole proteome modification landscape in a blind manner. The open database search is an efficient attempt to address this challenge by identifying peptides with mass shifts corresponding to possible modifications. Then, interpreting these mass shifts is required. Therefore, development of bioinformatics software for post-processing of the open search results, which is capable of detection and accurate annotation of new or unexpected modifications, from characterization of sample preparation efficiency and quality control to discovery of rare post-translational modifications, is of high importance.
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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 for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, 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, 119334 Moscow, 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, 119334 Moscow, Russia
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia.
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Murphy EL, Joy AP, Ouellette RJ, Barnett DA. Optimization of cysteine residue alkylation using an on-line LC-MS strategy: Benefits of using a cocktail of haloacetamide reagents. Anal Biochem 2021; 619:114137. [PMID: 33582115 DOI: 10.1016/j.ab.2021.114137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/31/2022]
Abstract
Several common reagents for the alkylation of cysteine residues of model intact proteins were evaluated for reaction speed, yield of alkylated product and degree of over-alkylation using an online LC-MS platform. The efficiency of the alkylation reaction is found to be dependent on the (1) reagent, (2) peptide/protein, (3) reagent concentration and (4) reaction time. At high reagent concentrations, iodoacetic acid was found to produce significant levels of over-alkylation products wherein methionine residues become modified. For optimal performance of the alkylation reaction, we found the use of a cocktail of chloroacetamide, bromoacetamide and iodoacetamide worked best. The alkylating efficiency of each haloacetamide is a balance between the characteristics of the halogen leaving group and the steric hindrance of the alkylation site on the peptide or protein. A key aspect of using a cocktail of haloacetamides is that they all produce the same modification (+57.0209 Da) to the cysteine residues of the protein while the alkylation efficiency of each site may differ for each of the three reagents. Over-alkylation effects appear to be lower with the cocktail due to a lower concentration of each reagent. The haloacetamide cocktail could be useful when considering complex mixtures of proteins.
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Affiliation(s)
- EmmaRae L Murphy
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada; Department of Process Engineering and Applied Science, Dalhousie University, Sexton Campus Chemical Engineering Building, PO Box 15000, Halifax, Nova Scotia, B3H4R2, Canada
| | - Andrew P Joy
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada
| | - Rodney J Ouellette
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada
| | - David A Barnett
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada; Department of Chemistry and Biochemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L1G8, Canada.
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