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Melendez C, Sanders J, Yilmaz M, Bittremieux W, Fondrie WE, Oh S, Noble WS. Accounting for Digestion Enzyme Bias in Casanovo. J Proteome Res 2024. [PMID: 39213590 DOI: 10.1021/acs.jproteome.4c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
A key parameter of any bottom-up proteomics mass spectrometry experiment is the identity of the enzyme that is used to digest proteins in the sample into peptides. The Casanovo de novo sequencing model was trained using data that was generated with trypsin digestion; consequently, the model prefers to predict peptides that end with the amino acids "K" or "R". This bias is desirable when Casanovo is used to analyze data that was also generated using trypsin but can be problematic if the data was generated using some other digestion enzyme. In this work, we modify Casanovo to take as input the identity of the digestion enzyme alongside each observed spectrum. We then train Casanovo with data generated by using several different enzymes, and we demonstrate that the resulting model successfully learns to capture enzyme-specific behavior. However, we find, surprisingly, that this new model does not yield a significant improvement in sequencing accuracy relative to a model trained without enzyme information but using the same training set. This observation may have important implications for future attempts to make use of experimental metadata in de novo sequencing models.
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Affiliation(s)
- Carlo Melendez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Justin Sanders
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Melih Yilmaz
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
| | | | - Sewoong Oh
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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2
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Lu X, Cummings C, Osuala UA, Yennawar NH, Namitz KEW, Hellner B, Besada-Lombana PB, Peterson RD, Clark AJ. Characterization of recombinant human lactoferrin expressed in Komagataella phaffii. Analyst 2024; 149:3636-3650. [PMID: 38814097 PMCID: PMC11215759 DOI: 10.1039/d4an00333k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
This work presents a thorough characterization of Helaina recombinant human lactoferrin (rhLF, Effera™) expressed in a yeast system at an industrial scale for the first time. Proteomic analysis confirmed that its amino acid sequence is identical to that of native human LF. N-linked glycans were detected at three known glycosylation sites, namely, Asparagines-156, -497, and -642 and they were predominantly oligomannose structures having five to nine mannoses. Helaina rhLF's protein secondary structure was nearly identical to that of human milk lactoferrin (hmLF), as revealed by microfluidic modulation spectroscopy. Results of small-angle X-ray scattering (SAXS) and analytical ultracentrifugation analyses confirmed that, like hmLF, Helaina rhLF displayed well-folded globular structures in solution. Reconstructed solvent envelopes of Helaina rhLF, obtained through the SAXS analysis, demonstrated a remarkable fit with the reported crystalline structure of iron-bound native hmLF. Differential scanning calorimetry investigations into the thermal stability of Helaina rhLF revealed two distinct denaturation temperatures at 68.7 ± 0.9 °C and 91.9 ± 0.5 °C, consistently mirroring denaturation temperatures observed for apo- and holo-hmLF. Overall, Helaina rhLF differed from hmLF in the N-glycans they possessed; nevertheless, the characterization results affirmed that Helaina rhLF was of high purity and exhibited globular structures closely akin to that of hmLF.
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Affiliation(s)
- Xiaoning Lu
- Helaina Inc., 345 Park Avenue South, 5th Floor, New York, NY 10010, USA.
| | - Chad Cummings
- Helaina Inc., 345 Park Avenue South, 5th Floor, New York, NY 10010, USA.
| | - Udodili A Osuala
- Helaina Inc., 345 Park Avenue South, 5th Floor, New York, NY 10010, USA.
| | - Neela H Yennawar
- X-ray Crystallography Core Facility, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin E W Namitz
- X-ray Crystallography Core Facility, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Brittney Hellner
- Helaina Inc., 345 Park Avenue South, 5th Floor, New York, NY 10010, USA.
| | | | - Ross D Peterson
- Helaina Inc., 345 Park Avenue South, 5th Floor, New York, NY 10010, USA.
| | - Anthony J Clark
- Helaina Inc., 345 Park Avenue South, 5th Floor, New York, NY 10010, USA.
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3
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Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
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Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
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4
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Melfi MT, Kanawati B, Schmitt-Kopplin P, Macchia L, Centonze D, Nardiello D. Investigation of fennel protein extracts by shot-gun Fourier transform ion cyclotron resonance mass spectrometry. Food Res Int 2021; 139:109919. [PMID: 33509486 DOI: 10.1016/j.foodres.2020.109919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/03/2020] [Accepted: 11/21/2020] [Indexed: 10/22/2022]
Abstract
A rapid shot-gun method by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is proposed for the characterization of fennel proteins. After enzymatic digestion with trypsin, few microliters of extract were analyzed by direct infusion in positive ion mode. A custom-made non-redundant fennel-specific proteome database was derived from the well-known NCBI database; additional proteins belonging to recognized allergenic sources (celery, carrot, parsley, birch, and mugwort) were also included in our database, since patients hypersensitive to these plants could also suffer from fennel allergy. The peptide sequence of each protein from that derived list was theoretically sequenced to produce calculated m/z lists of possible m/z ions after tryptic digestions. Then, by using a home-made Matlab algorithm, those lists were matched with the experimental FT-ICR mass spectrum of the fennel peptide mixture. Finally, Peptide Mass Fingerprint searches confirmed the presence of the matched proteins inside the fennel extract with a total of 70 proteins (61 fennel specific and 9 allergenic proteins).
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Affiliation(s)
- Maria Teresa Melfi
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Basem Kanawati
- Research Unit Analytical BioGeoChemistry (BGC), Helmholtz Zentrum München, Ingolstaedter Landstrasse, 85764 Neuherberg, Germany.
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry (BGC), Helmholtz Zentrum München, Ingolstaedter Landstrasse, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University of Munich, Alte Akademie 10, D-85354 Freising, Germany
| | - Luigi Macchia
- Dipartimento dell'Emergenza e dei Trapianti di Organi, Sezione di Allergologia ed Immunologia Clinica, Università degli Studi di Bari, Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Diego Centonze
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Donatella Nardiello
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy.
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5
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Calvano CD, Rigante ECL, Cataldi TRI, Sabbatini L. In Situ Hydrogel Extraction with Dual-Enzyme Digestion of Proteinaceous Binders: the Key for Reliable Mass Spectrometry Investigations of Artworks. Anal Chem 2020; 92:10257-10261. [PMID: 32648736 DOI: 10.1021/acs.analchem.0c01898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel strategy based on in situ dual-enzyme digestion of paint layer proteinaceous binders is introduced for faster and more confident identification, resulting in a bottom-up proteomics approach by MALDI-TOF mass spectrometry (MS). In situ sampling/extraction of proteinaceous binders using small pieces of a hydrophilic gel, previously loaded with trypsin and chymotrypsin proteolytic enzymes, was successfully exploited. Along with minimal invasiveness, the synergy of both enzymes was very useful to increase the number of annotated peptide peaks with their corresponding amino acid sequence by database search and subsequent MALDI-TOF/TOF analysis. The protocol was initially aimed at enhancing the identification of egg-based binders and then validated on fresh and aged model pictorial layers; an increased protein coverage was significantly attained regardless of the used painting binders. Optical microscope images and spectrophotocolorimetry analysis evidenced that the painting layers were not damaged or altered because of contact/sampling without leaving hydrogel residues. The proposed protocol was successfully applied on a painted altarpiece "Assumption of the Virgin" dated to the XVI century and on an angel statue of the Nativity crib dated to the XII century, both from Altamura's Cathedral (Apulia, Italy). The occurrence of various protein binders of animal origin was easily and reliably ascertained.
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6
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Melfi MT, Nardiello D, Natale A, Quinto M, Centonze D. An automated food protein isolation approach on preparative scale by two‐dimensional liquid chromatography with active modulation interface. Electrophoresis 2018; 40:1096-1106. [DOI: 10.1002/elps.201800500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Maria Teresa Melfi
- Dipartimento di Scienze Agrariedegli Alimenti e dell'AmbienteUniversità degli Studi di Foggia Foggia Italy
| | - Donatella Nardiello
- Dipartimento di Scienze Agrariedegli Alimenti e dell'AmbienteUniversità degli Studi di Foggia Foggia Italy
| | - Anna Natale
- Dipartimento di Scienze Agrariedegli Alimenti e dell'AmbienteUniversità degli Studi di Foggia Foggia Italy
| | - Maurizio Quinto
- Dipartimento di Scienze Agrariedegli Alimenti e dell'AmbienteUniversità degli Studi di Foggia Foggia Italy
| | - Diego Centonze
- Dipartimento di Scienze Agrariedegli Alimenti e dell'AmbienteUniversità degli Studi di Foggia Foggia Italy
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7
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Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
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Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
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8
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Naldi M, Tramarin A, Bartolini M. Immobilized enzyme-based analytical tools in the -omics era: Recent advances. J Pharm Biomed Anal 2018; 160:222-237. [DOI: 10.1016/j.jpba.2018.07.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023]
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9
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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10
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Nardiello D, Natale A, Palermo C, Quinto M, Centonze D. Milk authenticity by ion-trap proteomics following multi-enzyme digestion. Food Chem 2017; 244:317-323. [PMID: 29120788 DOI: 10.1016/j.foodchem.2017.10.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 09/26/2017] [Accepted: 10/09/2017] [Indexed: 01/14/2023]
Abstract
The practice of adding adulterating substances in milk in order to raise profits is unfortunately worldwide. In addition, higher priced milk, coming from minor dairy species, is often illegally integrated with the lower priced cow milk. The presence of species-specific proteins, different from those declared in label, may be a serious problem for people with allergies. The development of proper analytical methods is therefore essential to protect consumer benefits and product authenticity. In this study, a proteomic approach for the detection of adulteration processes of specific milks in mixtures is proposed. Few microliters of milk samples have been digested with trypsin and chymotrypsin and analyzed by nanoLC-ESI-IT-MS/MS. A post-database processing was performed to obtain confident peptide sequence assignments, allowing the detection of milk adulteration at a level lower than 1%. Species-specific peptides from bovine β-lactoglobulin and αS1 casein were identified as suitable peptide markers of milk authenticity.
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Affiliation(s)
- Donatella Nardiello
- Dipartimento di Scienze Agrarie, Degli Alimenti e dell'Ambiente, Università Degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy.
| | - Anna Natale
- Dipartimento di Scienze Agrarie, Degli Alimenti e dell'Ambiente, Università Degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Carmen Palermo
- Dipartimento di Scienze Agrarie, Degli Alimenti e dell'Ambiente, Università Degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Maurizio Quinto
- Dipartimento di Scienze Agrarie, Degli Alimenti e dell'Ambiente, Università Degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Diego Centonze
- Dipartimento di Scienze Agrarie, Degli Alimenti e dell'Ambiente, Università Degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
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11
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Nardiello D, Prattichizzo C, Rocchetti MT, Gesualdo L, Centonze D. Nano-LC-MS/MS for the identification of proteins trapped in sorbent cartridges used for coupled plasma filtration-adsorption treatments of healthy pigs. J Pharm Biomed Anal 2017; 132:215-222. [PMID: 27768920 DOI: 10.1016/j.jpba.2016.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/05/2016] [Accepted: 10/09/2016] [Indexed: 11/25/2022]
Abstract
A dedicated proteomic approach based on nano-Liquid Chromatography coupled with tandem mass spectrometry in ion trap is proposed for the analysis of proteins trapped in sorbent resin cartridges used to remove inflammatory mediators from blood by coupled plasma filtration adsorption (CPFA). The final purpose of the proposed proteomic approach was to obtain a reference map of plasma proteins trapped in CPFA sorbents used for the extracorporeal blood purification of healthy pigs, with the potential impact to design new bio-filters able to control the inflammatory imbalance under pathological conditions, such as severe sepsis. The five main steps of the proteomics analysis, (i) protein extraction from resin cartridges, (ii) two-dimensional gel electrophoresis (2D-PAGE) for protein separation and profiling, (iii) in-gel proteolytic digestion, (iv) tandem mass analysis of peptides resulting from enzymatic cleavage and (v) bioinformatics, for protein identification and post-processing validation of MS/MS data sets, have been carefully evaluated. Prior to electrophoresis, the efficiency of different extraction solutions and procedures to recovery plasma proteins trapped into the sorbents were tested. Then, a rapid one-step procedure for protein extraction was optimized. Protein bands corresponding to the main plasma proteins, namely porcine serum albumin, serotransferrin and immunoglobulins, were identified. In addition, the presence of haptoglobin, hemopexin, α-1 acid glycoprotein and fetuin-A, that are known as acute-phase reaction proteins, was observed, suggesting that CPFA resins led to a non-specifically protein depletion from plasma, rather than targeting specific molecules.
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Affiliation(s)
- Donatella Nardiello
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente and CSRA- Centro Servizi di Ricerca Applicata, Università degli Studi di Foggia, Via Napoli, 25 - 71122 Foggia, Italy.
| | - Clelia Prattichizzo
- Dipartimento di Scienze Mediche e Chirurgiche, Sezione di Nefrologia, Dialisi e Trapianto, Università degli Studi di Foggia, Viale Luigi Pinto, 1 - 71122 Foggia, Italy
| | - Maria Teresa Rocchetti
- Dipartimento di Emergenza e Trapianti di Organi, Università degli Studi di Bari, Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Loreto Gesualdo
- Dipartimento di Emergenza e Trapianti di Organi, Università degli Studi di Bari, Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Diego Centonze
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente and CSRA- Centro Servizi di Ricerca Applicata, Università degli Studi di Foggia, Via Napoli, 25 - 71122 Foggia, Italy
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12
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Nardiello D, Natale A, Palermo C, Quinto M, Centonze D. Combined use of peptide ion and normalized delta scores to evaluate milk authenticity by ion-trap based proteomics coupled with error tolerant searching. Talanta 2016; 164:684-692. [PMID: 28107990 DOI: 10.1016/j.talanta.2016.10.102] [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] [Received: 06/30/2016] [Revised: 10/25/2016] [Accepted: 10/30/2016] [Indexed: 12/17/2022]
Abstract
A fundamental issue in proteomics is the peptide identification by database searching and the assessment of the goodness of fit between experimental and theoretical data. Despite the different number of ways to measure the quality of search results, the definition of a scoring criterion is still highly desirable in ion-trap based proteomics. Indeed, in order to fully take advantage of a low resolution MS/MS dataset, it is essential to strike a balance between greater information capture and reduced number of incorrect peptide assignments. In addition, the development of user-specified rules is a crucial aspect when very similar proteins of the same family are analyzed in order to infer the origin species. In this study, a post-processing validation scheme is provided for the evaluation of proteomic data in shot-gun ion-trap proteomics, when a flexible database searching based on the error tolerant mode is adopted in combination with a low-specificity enzyme to maximize sequence coverage. To validate peptide assignments, we used standard β-casein digested with trypsin/chymotrypsin or trypsin alone and the popular search engine MASCOT to identify the relevant (known) peptide sequences. A linear combination between peptide ion score and normalized delta score (i.e. the difference between the best and the second best ion score, divided by the best score) is proposed to increase the accuracy in sequence assignments from low-resolution tandem mass spectra. Finally, the optimized post-processing database validation was successfully applied to the direct analysis of milk tryptic/chymotryptic digests of different origin, without resorting to two-dimensional electrophoresis that is usually performed for protein separation in ion-trap proteomics. The identification of species-specific amino acidic sequences among the validated peptide spectrum matches has allowed to fully discriminate between the animal species, so evaluating accurately the milk authenticity.
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Affiliation(s)
- Donatella Nardiello
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente and CSRA, Centro Servizi di Ricerca Applicata, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy.
| | - Anna Natale
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente and CSRA, Centro Servizi di Ricerca Applicata, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Carmen Palermo
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente and CSRA, Centro Servizi di Ricerca Applicata, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Maurizio Quinto
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente and CSRA, Centro Servizi di Ricerca Applicata, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Diego Centonze
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente and CSRA, Centro Servizi di Ricerca Applicata, Università degli Studi di Foggia, Via Napoli, 25, 71122 Foggia, Italy
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13
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Yu H, Huang T. Molecular Mechanisms of Floral Boundary Formation in Arabidopsis. Int J Mol Sci 2016; 17:317. [PMID: 26950117 PMCID: PMC4813180 DOI: 10.3390/ijms17030317] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 01/03/2023] Open
Abstract
Boundary formation is a crucial developmental process in plant organogenesis. Boundaries separate cells with distinct identities and act as organizing centers to control the development of adjacent organs. In flower development, initiation of floral primordia requires the formation of the meristem-to-organ (M-O) boundaries and floral organ development depends on the establishment of organ-to-organ (O-O) boundaries. Studies in this field have revealed a suite of genes and regulatory pathways controlling floral boundary formation. Many of these genes are transcription factors that interact with phytohormone pathways. This review will focus on the functions and interactions of the genes that play important roles in the floral boundaries and discuss the molecular mechanisms that integrate these regulatory pathways to control the floral boundary formation.
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Affiliation(s)
- Hongyang Yu
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
- College of Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
| | - Tengbo Huang
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
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14
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Wang Y, Han Y, Fan E, Zhang K. Analytical strategies used to identify the readers of histone modifications: A review. Anal Chim Acta 2015; 891:32-42. [PMID: 26388362 DOI: 10.1016/j.aca.2015.06.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
Abstract
The so-called "readers" of histone post-translational modifications (HPTMs) refer to proteins or complexes that are recruited to HPTMs thus eventually regulate gene transcription. To identify these "readers", mass spectrometry plays an essential role following various enriching strategies. These enriching methods include the use of modified histone peptides/proteins or chemically synthesized histones/nucleosomes containing desired HPTMs to enrich the readers of HPTMs. Despite the peptide- or protein-based assay is straightforward and easy to perform for most labs, this strategy has limited applications for those weak or combinational interactions among various HPTMs and false-positive results are a potential big problem. While the results derived from synthesized histone proteins/nucleosomes is more reliable as it mimics the real chromatic conditions thus is able to analyze the binders of those cross-talked HPTMs, usually the synthesis is so difficult that their applications are impeded for high throughput analysis. In this review, an overview of these analytical techniques is provided and their advantages and disadvantages are discussed.
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Affiliation(s)
- Ye Wang
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Yanpu Han
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany; School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Jungong Road No. 516, 200093 Shanghai, China.
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, 300070 Tianjin, China; Department of Chemistry, Nankai University, 300071 Tianjin, China.
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15
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Yang L, Lian X, Zhang W, Guo J, Wang Q, Li Y, Chen Y, Yin X, Yang P, Lan F, He QY, Zhang G, Wang T. Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria. J Proteome Res 2015. [DOI: 10.1021/acs.jproteome.5b00480] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lijuan Yang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xinlei Lian
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wanling Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jie Guo
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yang Chen
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xingfeng Yin
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | | | | | - Qing-Yu He
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
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16
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Integrated SDS removal and protein digestion by hollow fiber membrane based device for SDS-assisted proteome analysis. Talanta 2015; 141:235-8. [DOI: 10.1016/j.talanta.2015.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/30/2015] [Accepted: 04/05/2015] [Indexed: 11/18/2022]
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