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Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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Nicoletti M, Gambarotti C, Fasoli E. Proteomic fingerprinting of protein corona formed on PEGylated multi-walled carbon nanotubes. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1163:122504. [PMID: 33412504 DOI: 10.1016/j.jchromb.2020.122504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 01/10/2023]
Abstract
In Nanomedicine, carbon-based nanomaterials, like Carbon Nanotubes (CNT), are considered potential candidates as drug delivery systems. In vivo adsorption of physiological proteins onto carbon nanotubes, through noncovalent interactions, forms a protein corona or bio corona, able to influence biological properties and biocompatibility of CNT. This study aimed to explore the composition of protein corona formed onto PEGylated Multi-Walled Carbon Nanotubes (MWCNT-PEG5k), after their incubation in human plasma. Plasma proteins were sequentially eluted in different conditions by using both native and denaturant buffers, useful to characterize soft and hard corona. Proteomic methods and mass spectrometry analysis have identified proteins in soft corona, involved in the regulation of immune response and in the CNT transport, and biomolecules in hard corona with a role in the maintenance of host homeostasis. These promising results have demonstrated the potential of PEGylated Multi-Walled Carbon Nanotubes as future candidates for drug delivery.
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Affiliation(s)
- Maria Nicoletti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Cristian Gambarotti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
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Nicoletti M, Gambarotti C, Fasoli E. Proteomic exploration of soft and hard biocorona onto PEGylated multiwalled carbon nanotubes. Biotechnol Appl Biochem 2020; 68:1003-1013. [PMID: 32910836 DOI: 10.1002/bab.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/31/2020] [Indexed: 01/03/2023]
Abstract
In nanomedicine, carbon nanotubes (CNTs) are considered potential candidates as drug delivery systems. The absorption of proteins onto CNTs, after their administration in physiological environment, forms the protein corona or biocorona, which is able to influence their biological properties and biocompatibility. For this reason, characterization of protein corona is a crucial aspect in the research to control CNTs toxicity and capability to target cells. Multiwalled carbon nanotubes (MWCNTs) were functionalized with polyethylene glycol (PEG), chosen considering its well-known biocompatibility, and then incubated in human plasma to create the biocorona. Plasma proteins, which bound around PEGylated CNTs, were detached using five different solutions, grouped into native and denaturant buffers, and used to characterize the two components of biocorona. The proteomic fingerprinting of biocorona was performed by SDS-PAGE and 2D-PAGE separation and mass spectrometry analysis. Native eluents were able to capture proteins of soft corona, characterized by complex secondary structures, and formed by both β-sheet and α-helices domains. Denaturant buffers have eluted many proteins with a high percentage of the α-helix structure that could be involved in specific interactions responsible for the formation of hard corona.
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Affiliation(s)
- Maria Nicoletti
- Department of Chemistry, Materials and Chemical Engineering, "Giulio Natta,", Politecnico di Milano, Milan, 20133, Italy
| | - Cristian Gambarotti
- Department of Chemistry, Materials and Chemical Engineering, "Giulio Natta,", Politecnico di Milano, Milan, 20133, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering, "Giulio Natta,", Politecnico di Milano, Milan, 20133, Italy
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Boschetti E, Righetti PG. Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods. Methods Mol Biol 2020; 2139:381-404. [PMID: 32462601 DOI: 10.1007/978-1-0716-0528-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries. This methodology, allowing for an enhancement of low-abundance proteins, has been extensively applied with the advantage of deciphering the proteome composition of various plant organs. This general methodology is here described extensively along with a number of possible variations. Specific guidelines are suggested to cover peculiar situations or to comply with other associated analytical methods.
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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Zasada M, Suski M, Bokiniec R, Szwarc-Duma M, Borszewska-Kornacka MK, Madej J, Bujak-Giżycka B, Madetko-Talowska A, Revhaug C, Baumbusch LO, Saugstad OD, Pietrzyk JJ, Kwinta P. Comparative two time-point proteome analysis of the plasma from preterm infants with and without bronchopulmonary dysplasia. Ital J Pediatr 2019; 45:112. [PMID: 31445514 PMCID: PMC6708124 DOI: 10.1186/s13052-019-0676-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Background In this study, we aimed to analyze differences in plasma protein abundances between infants with and without bronchopulmonary dysplasia (BPD), to add new insights into a better understanding of the pathogenesis of this disease. Methods Cord and peripheral blood of neonates (≤ 30 weeks gestational age) was drawn at birth and at the 36th postmenstrual week (36 PMA), respectively. Blood samples were retrospectively subdivided into BPD(+) and BPD(−) groups, according to the development of BPD. Results Children with BPD were characterized by decreased afamin, gelsolin and carboxypeptidase N subunit 2 levels in cord blood, and decreased galectin-3 binding protein and hemoglobin subunit gamma-1 levels, as well as an increased serotransferrin abundance in plasma at the 36 PMA. Conclusions BPD development is associated with the plasma proteome changes in preterm infants, adding further evidence for the possible involvement of disturbances in vitamin E availability and impaired immunological processes in the progression of prematurity pulmonary complications. Moreover, it also points to the differences in proteins related to infection resistance and maintaining an adequate level of hematocrit in infants diagnosed with BPD.
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Affiliation(s)
- Magdalena Zasada
- Department of Pediatrics, Jagiellonian University Medical College, Cracow, Poland
| | - Maciej Suski
- Chair of Pharmacology, Jagiellonian University Medical College, Cracow, Poland
| | - Renata Bokiniec
- Neonatal and Intensive Care Department, Medical University of Warsaw, Warsaw, Poland
| | - Monika Szwarc-Duma
- Neonatal and Intensive Care Department, Medical University of Warsaw, Warsaw, Poland
| | | | - Józef Madej
- Chair of Pharmacology, Jagiellonian University Medical College, Cracow, Poland
| | - Beata Bujak-Giżycka
- Chair of Pharmacology, Jagiellonian University Medical College, Cracow, Poland
| | - Anna Madetko-Talowska
- Department of Medical Genetics, Jagiellonian University Medical College, Cracow, Poland
| | - Cecilie Revhaug
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Lars O Baumbusch
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Ola D Saugstad
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway. .,University of Oslo, Oslo, Norway.
| | - Jacek Józef Pietrzyk
- Department of Pediatrics, Jagiellonian University Medical College, Cracow, Poland
| | - Przemko Kwinta
- Department of Pediatrics, Jagiellonian University Medical College, Cracow, Poland
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Zasada M, Suski M, Bokiniec R, Szwarc-Duma M, Borszewska-Kornacka MK, Madej J, Bujak-Gizycka B, Madetko-Talowska A, Revhaug C, Baumbusch LO, Saugstad OD, Pietrzyk JJ, Kwinta P. An iTRAQ-Based Quantitative Proteomic Analysis of Plasma Proteins in Preterm Newborns With Retinopathy of Prematurity. Invest Ophthalmol Vis Sci 2019; 59:5312-5319. [PMID: 30398622 DOI: 10.1167/iovs.18-24914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Retinopathy of prematurity (ROP) is a vision-threatening complication of a premature birth, in which the etiology still remains unclear. Importantly, the molecular processes that govern these effects can be investigated in a perturbed plasma proteome composition. Thus, plasma proteomics may add new insights into a better understanding of the pathogenesis of this disease. Methods The cord and peripheral blood of neonates (≤30 weeks gestational age) was drawn at birth and at the 36th postmenstrual week (PMA), respectively. Blood samples were retrospectively subdivided into ROP(+) and ROP(-) groups, according to the development of ROP. Results The quantitative analysis of plasma proteome at both time points revealed 30 protein abundance changes between ROP(+) and ROP(-) groups. After standardization to gestational age, children who developed ROP were characterized by an increased C3 complement component and fibrinogen level at both analyzed time points. Conclusions Higher levels of the complement C3 component and fibrinogen, present in the cord blood and persistent to 36 PMA, may indicate a chronic low-grade systemic inflammation and hypercoagulable state that may play a role in the development of ROP.
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Affiliation(s)
- Magdalena Zasada
- Department of Pediatrics, Jagiellonian University Medical College, Krakow, Poland
| | - Maciej Suski
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Renata Bokiniec
- Neonatal and Intensive Care Department, Medical University of Warsaw, Warsaw, Poland
| | - Monika Szwarc-Duma
- Neonatal and Intensive Care Department, Medical University of Warsaw, Warsaw, Poland
| | | | - Józef Madej
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Beata Bujak-Gizycka
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Anna Madetko-Talowska
- Department of Medical Genetics, Jagiellonian University Medical College, Krakow, Poland
| | - Cecilie Revhaug
- Department of Pediatric Research, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Lars O Baumbusch
- Department of Pediatric Research, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Ola D Saugstad
- Department of Pediatric Research, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Jacek Józef Pietrzyk
- Department of Pediatrics, Jagiellonian University Medical College, Krakow, Poland
| | - Przemko Kwinta
- Department of Pediatrics, Jagiellonian University Medical College, Krakow, Poland
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Boschetti E, Hernández-Castellano LE, Righetti PG. Progress in farm animal proteomics: The contribution of combinatorial peptide ligand libraries. J Proteomics 2019; 197:1-13. [DOI: 10.1016/j.jprot.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/17/2019] [Accepted: 02/07/2019] [Indexed: 02/08/2023]
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Sánchez-Juanes F, González-Buitrago JM. Sample Treatment for Urine Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:125-135. [PMID: 31236841 DOI: 10.1007/978-3-030-12298-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Urine is a biological fluid that can be collected noninvasively in relatively large quantities which can be used for the search of biomarkers of disease, both diseases of the urological tract and systemic diseases. One of the most important aspects in proteomic studies is sample treatment before further analysis. Methods of preparation of a urine sample depend on the techniques that will be used later for separation and identification of the proteins. Also, urine preparation should be as simple as possible to increase reproducibility. Normal urine has a much diluted protein concentration with a high-salt content, which interferes with proteomic analysis. Thus, an initial step in the handling of urine sample should be to concentrate and eliminate salts. As range of protein concentrations in urine spans several orders of magnitude, effective proteomic analyses require either removal of most abundant protein or enrichment of the less abundant ones. In this chapter, we discuss the aspects related to the collection and treatment of urine for proteomic studies.
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Affiliation(s)
- Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Salamanca, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain
| | - José Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Salamanca, Spain. .,Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain. .,Servicio de Análisis Clínicos/Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain.
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Lerma-García MJ, Nicoletti M, Simó-Alfonso EF, Righetti PG, Fasoli E. Proteomic fingerprinting of apple fruit, juice, and cider via combinatorial peptide ligand libraries and MS analysis. Electrophoresis 2018; 40:266-271. [DOI: 10.1002/elps.201800320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 12/15/2022]
Affiliation(s)
| | - Maria Nicoletti
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan Italy
| | | | - Pier Giorgio Righetti
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan Italy
| | - Elisa Fasoli
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan Italy
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Plasma proteome changes in cord blood samples from preterm infants. J Perinatol 2018; 38:1182-1189. [PMID: 29910464 DOI: 10.1038/s41372-018-0150-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 01/23/2023]
Abstract
OBJECTIVE In the presented study, we aimed to systematically analyze plasma proteomes in cord blood samples from preterm infants stratified by their gestational age to identify proteins and related malfunctioning pathways at birth, possibly contributing to the complications observed among preterm infants. STUDY DESIGN Preterm newborns were enrolled of three subgroups with different gestation age: newborns born ≤26 (group 1), between 27 and 28 (group 2) and between 29 and 30 (group 3) weeks of gestation, respectively, and compared to the control group of healthy, full-term newborns in respect to their plasma proteome composition. RESULT Preterm delivery is associated with multiple protein abundance changes in plasma related to a plethora of processes, including inflammation and immunomodulation, coagulation, and complement activation as some key features. CONCLUSION Plasma proteome analysis revealed numerous gestation-age-dependent protein abundance differences between term and preterm infants, which highlight key dysregulated pathways and potential new protein treatment targets.
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12
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Nicoletti M, Capodanno C, Gambarotti C, Fasoli E. Proteomic investigation on bio-corona of functionalized multi-walled carbon nanotubes. Biochim Biophys Acta Gen Subj 2018; 1862:2293-2303. [PMID: 30048739 DOI: 10.1016/j.bbagen.2018.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND The formation of bio-corona, due to adsorption of biomolecules onto carbon nanotubes (CNTs) surface in a physiological environment, may lead to a modified biological "identity" of CNTs, contributing to determination of their biocompatibility and toxicity. METHODS Multi-walled carbon nanotubes surfaces (f-MWCNTs) were modified attaching acid and basic chemical functions such as carboxyl (MWCNTs-COOH) and ammonium (MWCNTs-N) groups respectively. The investigation of interactions between f-MWCNTs and proteins present in biological fluids, like human plasma, was performed by electrophoretic separation (SDS-PAGE) and mass spectrometry analysis (nLC-MS/MS). RESULTS A total of 52 validated proteins was identified after incubation of f-MWCNTs in human plasma. 86% of them was present in bio-coronas formed on the surface of all f-MWCNTs and 29% has specifically interacted with only one type of f-MWCNTs. CONCLUSIONS The evaluation of proteins primary structures, present in all bio-coronas, did not highlight any correlation between the chemical functionalization on MWCNTs and the content of acid, basic and hydrophobic amino acids. Despite this, many proteins of bio-corona, formed on all f-MWCNTs, were involved in the inhibitor activity of serine- or cysteine- endopeptidases, a molecular function completely unrevealed in the human plasma as control. Finally, the interaction with immune system's proteins and apolipoproteins has suggested a possible biocompatibility and a favored bio-distribution of tested f-MWCNTs. GENERAL SIGNIFICANCE Considering the great potential of CNTs in the nanomedicine, a specific chemical functionalization onto MWCNTs surface could control the protein corona formation and the biocompatibility of nanomaterials.
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Affiliation(s)
- Maria Nicoletti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131 Milan, Italy
| | - Claudia Capodanno
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131 Milan, Italy
| | - Cristian Gambarotti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131 Milan, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131 Milan, Italy.
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Harpole M, Davis J, Espina V. Current state of the art for enhancing urine biomarker discovery. Expert Rev Proteomics 2017; 13:609-26. [PMID: 27232439 DOI: 10.1080/14789450.2016.1190651] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Urine is a highly desirable biospecimen for biomarker analysis because it can be collected recurrently by non-invasive techniques, in relatively large volumes. Urine contains cellular elements, biochemicals, and proteins derived from glomerular filtration of plasma, renal tubule excretion, and urogenital tract secretions that reflect, at a given time point, an individual's metabolic and pathophysiologic state. AREAS COVERED High-resolution mass spectrometry, coupled with state of the art fractionation systems are revealing the plethora of diagnostic/prognostic proteomic information existing within urinary exosomes, glycoproteins, and proteins. Affinity capture pre-processing techniques such as combinatorial peptide ligand libraries and biomarker harvesting hydrogel nanoparticles are enabling measurement/identification of previously undetectable urinary proteins. Expert commentary: Future challenges in the urinary proteomics field include a) defining either single or multiple, universally applicable data normalization methods for comparing results within and between individual patients/data sets, and b) defining expected urinary protein levels in healthy individuals.
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Affiliation(s)
- Michael Harpole
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin Davis
- b Department of Chemistry/Biochemistry , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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Zavvos V, Buxton AT, Evans C, Lambie M, Davies SJ, Topley N, Wilkie M, Summers A, Brenchley P, Goumenos DS, Johnson TS. A prospective, proteomics study identified potential biomarkers of encapsulating peritoneal sclerosis in peritoneal effluent. Kidney Int 2017; 92:988-1002. [PMID: 28673451 DOI: 10.1016/j.kint.2017.03.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 03/14/2017] [Accepted: 03/16/2017] [Indexed: 11/28/2022]
Abstract
Encapsulating peritoneal sclerosis (EPS) is a potentially devastating complication of peritoneal dialysis (PD). Diagnosis is often delayed due to the lack of effective and accurate diagnostic tools. We therefore examined peritoneal effluent for potential biomarkers that could predict or confirm the diagnosis of EPS and would be valuable in stratifying at-risk patients and driving appropriate interventions. Using prospectively collected samples from the Global Fluid Study and a cohort of Greek PD patients, we utilized 2D SDSPAGE/ MS and iTRAQ to identify changes in the peritoneal effluent proteome from patients diagnosed with EPS and controls matched for treatment exposure. We employed a combinatorial peptide ligand library to compress the dynamic range of protein concentrations to aid identification of low-abundance proteins. In patients with stable membrane function, fibrinogen γ-chain and heparan sulphate proteoglycan core protein progressively increased over time on PD. In patients who developed EPS, collagen-α1(I), γ-actin and Complement factors B and I were elevated up to five years prior to diagnosis. Orosomucoid-1 and a2-HS-glycoprotein chain-B were elevated about one year before diagnosis, while apolipoprotein A-IV and α1-antitrypsin were decreased compared to controls. Dynamic range compression resulted in an increased number of proteins detected with improved resolution of protein spots, compared to the full fluid proteome. Intelectin-1, dermatopontin, gelsolin, and retinol binding protein-4 were elevated in proteome-mined samples from patients with EPS compared to patients that had just commenced peritoneal dialysis. Thus, prospective analysis of peritoneal effluent uncovered proteins indicative of inflammatory and pro-fibrotic injury worthy of further evaluation as diagnostic/prognostic markers.
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Affiliation(s)
- Vasileios Zavvos
- Department of Nephrology, University Hospital of Patras, Patras, Greece; Academic Nephrology Unit and Sheffield Kidney Institute, University of Sheffield, Sheffield, UK
| | - Anthony T Buxton
- Academic Nephrology Unit and Sheffield Kidney Institute, University of Sheffield, Sheffield, UK
| | - Caroline Evans
- Proteomics Unit, Chemical Engineering, University of Sheffield, Sheffield, UK
| | - Mark Lambie
- Institute of Applied Clinical Sciences, Keele University, Keele, UK
| | - Simon J Davies
- Institute of Applied Clinical Sciences, Keele University, Keele, UK
| | - Nicholas Topley
- Wales Kidney Research Unit, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Martin Wilkie
- Academic Nephrology Unit and Sheffield Kidney Institute, University of Sheffield, Sheffield, UK
| | - Angela Summers
- Kidney Research Laboratories, Manchester Royal Infirmary, Manchester, UK
| | - Paul Brenchley
- Kidney Research Laboratories, Manchester Royal Infirmary, Manchester, UK
| | | | - Timothy S Johnson
- Academic Nephrology Unit and Sheffield Kidney Institute, University of Sheffield, Sheffield, UK.
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Proteomic fingerprinting of mistletoe ( Viscum album L.) via combinatorial peptide ligand libraries and mass spectrometry analysis. J Proteomics 2017; 164:52-58. [DOI: 10.1016/j.jprot.2017.05.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/26/2017] [Accepted: 05/27/2017] [Indexed: 11/18/2022]
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16
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Polyphemus, Odysseus and the ovine milk proteome. J Proteomics 2017; 152:58-74. [DOI: 10.1016/j.jprot.2016.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/21/2016] [Accepted: 10/20/2016] [Indexed: 12/12/2022]
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Kachuk C, Faulkner M, Liu F, Doucette AA. Automated SDS Depletion for Mass Spectrometry of Intact Membrane Proteins though Transmembrane Electrophoresis. J Proteome Res 2016; 15:2634-42. [DOI: 10.1021/acs.jproteome.6b00199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Carolyn Kachuk
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Melissa Faulkner
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Fang Liu
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alan A. Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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18
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Proteomic characterization of hempseed (Cannabis sativa L.). J Proteomics 2016; 147:187-196. [PMID: 27265319 DOI: 10.1016/j.jprot.2016.05.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/17/2016] [Accepted: 05/31/2016] [Indexed: 02/08/2023]
Abstract
UNLABELLED This paper presents an investigation on hempseed proteome. The experimental approach, based on combinatorial peptide ligand libraries (CPLLs), SDS-PAGE separation, nLC-ESI-MS/MS identification, and database search, permitted identifying in total 181 expressed proteins. This very large number of identifications was achieved by searching in two databases: Cannabis sativa L. (56 gene products identified) and Arabidopsis thaliana (125 gene products identified). By performing a protein-protein association network analysis using the STRING software, it was possible to build the first interactomic map of all detected proteins, characterized by 137 nodes and 410 interactions. Finally, a Gene Ontology analysis of the identified species permitted to classify their molecular functions: the great majority is involved in the seed metabolic processes (41%), responses to stimulus (8%), and biological process (7%). BIOLOGICAL SIGNIFICANCE Hempseed is an underexploited non-legume protein-rich seed. Although its protein is well known for its digestibility, essential amino acid composition, and useful techno-functional properties, a comprehensive proteome characterization is still lacking. The objective of this work was to fill this knowledge gap and provide information useful for a better exploitation of this seed in different food products.
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Gianazza E, Miller I, Palazzolo L, Parravicini C, Eberini I. With or without you — Proteomics with or without major plasma/serum proteins. J Proteomics 2016; 140:62-80. [DOI: 10.1016/j.jprot.2016.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/26/2022]
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20
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Weng Y, Sui Z, Shan Y, Jiang H, Zhou Y, Zhu X, Liang Z, Zhang L, Zhang Y. In-Depth Proteomic Quantification of Cell Secretome in Serum-Containing Conditioned Medium. Anal Chem 2016; 88:4971-8. [DOI: 10.1021/acs.analchem.6b00910] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yejing Weng
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yichu Shan
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jiang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Zhou
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xudong Zhu
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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21
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Orange proteomic fingerprinting: From fruit to commercial juices. Food Chem 2016; 196:739-49. [DOI: 10.1016/j.foodchem.2015.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/24/2015] [Accepted: 10/01/2015] [Indexed: 10/23/2022]
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22
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Thomas S, Hao L, Ricke WA, Li L. Biomarker discovery in mass spectrometry-based urinary proteomics. Proteomics Clin Appl 2016; 10:358-70. [PMID: 26703953 DOI: 10.1002/prca.201500102] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/05/2015] [Accepted: 12/21/2015] [Indexed: 01/03/2023]
Abstract
Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians.
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Affiliation(s)
- Samuel Thomas
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - William A Ricke
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Urology, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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23
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Colzani M, Altomare A, Caliendo M, Aldini G, Righetti PG, Fasoli E. The secrets of Oriental panacea: Panax ginseng. J Proteomics 2016; 130:150-9. [DOI: 10.1016/j.jprot.2015.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/11/2015] [Accepted: 09/17/2015] [Indexed: 02/05/2023]
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24
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Characterization of new outer membrane proteins of Pseudomonas aeruginosa using a combinatorial peptide ligand library. Anal Bioanal Chem 2015; 407:1513-8. [PMID: 25471289 DOI: 10.1007/s00216-014-8313-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Most often, the use of ProteoMiner beads has been restricted to human serum proteins for the normalization of major proteins, such as albumin. However, there are other situations of interest in which the presence of major proteins would quench the signals of low abundance polypeptides. We propose the use of these beads for investigating the envelope of the gram-negative bacterium Pseudomonas aeruginosa. Initially, we performed comparative 2D electrophoresis to qualitatively evaluate the incidence of the normalization stage. This demonstrated a significant reduction of the major membrane proteins. Thereafter, using shotgun analysis, the same protein extract was targeted by using combinatorial peptide ligand library capture. This treatment yielded 154 additional outer membrane proteins (OMPs) uncovered by the study of the crude sample.
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25
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Cunsolo V, Fasoli E, Saletti R, Muccilli V, Gallina S, Righetti PG, Foti S. Zeus, Aesculapius, Amalthea and the proteome of goat milk. J Proteomics 2015; 128:69-82. [DOI: 10.1016/j.jprot.2015.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
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26
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Candiano G, Santucci L, Petretto A, Lavarello C, Inglese E, Bruschi M, Ghiggeri GM, Boschetti E, Righetti PG. Widening and Diversifying the Proteome Capture by Combinatorial Peptide Ligand Libraries via Alcian Blue Dye Binding. Anal Chem 2015; 87:4814-20. [DOI: 10.1021/acs.analchem.5b00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Giovanni Candiano
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Laura Santucci
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Andrea Petretto
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Chiara Lavarello
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Elvira Inglese
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Maurizio Bruschi
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Gian Marco Ghiggeri
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | | | - Pier Giorgio Righetti
- Department
of Chemistry, Materials and Chemical Engineering, “Giulio
Natta”, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
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27
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Henning AK, Albrecht D, Riedel K, Mettenleiter TC, Karger A. An alternative method for serum protein depletion/enrichment by precipitation at mildly acidic pH values and low ionic strength. Proteomics 2015; 15:1935-40. [PMID: 25644273 DOI: 10.1002/pmic.201400257] [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: 06/05/2014] [Revised: 12/15/2014] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Serum proteome analysis is severely hampered by the extreme dynamic range of protein concentrations, but tools for the specific depletion of highly abundant serum proteins lack for most farm and companion animals. A well-established alternative strategy to reduce the dynamic range of plasma protein concentrations, treatment with combinatorial peptide ligand libraries (CPLL), is generally applicable but requires large amounts of sample. Therefore, additional depletion/enrichment protocols for plasma and serum samples from animals are desirable. In this respect, we have tested a protein precipitate that formed after withdrawal of salt from human, bovine, or porcine serum at pH 4.2. The bovine sample was composed of over 300 proteins making it a potential source for biomarker discovery. Precipitation was highly reproducible and the concentrations of albumin and other highly abundant serum proteins were strongly reduced. In comparison to the CPLL treatment, precipitation did not introduce any selection bias based on hydrophathy or pI. However, the composition of both preparations was partially complementary. Salt withdrawal at pH 4.2 is suggested as additional depletion/enrichment strategy for serum samples. Also, we point out that the removal of precipitates from serum samples under the described conditions bears the risk of losing a valuable protein fraction.
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Affiliation(s)
- Ann-Kristin Henning
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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28
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Bruschi M, Candiano G, Santucci L, D'Ambrosio C, Scaloni A, Bonsano M, Ghiggeri GM, Verrina E. Combinatorial Peptide Ligand Library and two dimensional electrophoresis: New frontiers in the study of peritoneal dialysis effluent in pediatric patients. J Proteomics 2015; 116:68-80. [DOI: 10.1016/j.jprot.2015.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/22/2014] [Accepted: 01/04/2015] [Indexed: 12/28/2022]
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29
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Boschetti E, Righetti PG. Mixed-bed affinity chromatography: principles and methods. Methods Mol Biol 2015; 1286:131-158. [PMID: 25749952 DOI: 10.1007/978-1-4939-2447-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mixed-bed chromatography is far from being a well-established technology within the panoply of bioseparation tools. Composed of an assembly of distinct sorbents that are mixed in a single bed, they have been mostly developed in the last decade for the reduction of dynamic concentration range where they allowed discovering many low-copy proteins within very complex proteomes. Other interesting preparative applications of mixed-bed chromatography have since been developed. In this chapter the basic concepts first and then detailed application recipes are described for (1) the reduction of protein dynamic concentration range, (2) the removal of impurity traces at the last stage of a biopurification process, and (3) the selection and use of sorbents as mixed bed in protein purification.
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Affiliation(s)
- Egisto Boschetti
- JAM-Conseil, 9-11 rue Boutard, 92200, Neuilly sur Seine, France,
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30
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Righetti PG, Boschetti E. Sample treatment methods involving combinatorial peptide ligand libraries for improved proteomes analyses. Methods Mol Biol 2015; 1243:55-82. [PMID: 25384740 DOI: 10.1007/978-1-4939-1872-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
If used in an optimized manner, the technology of combinatorial peptide solid-phase libraries can easily improve the analytical determinations of proteomes by several factors. The discovery of novel species and of early stage biomarkers becomes thus reachable with a simple sample treatment. This report describes the most important point to consider (overloading and full recovery) along with a minimum scientific background and gives then detailed recipes to laboratory technicians. Orientations for optional routes are also given according to the objective of the experimental investigations. This covers different approaches to capture proteins of very low abundance. Total protein harvestings to prevent partial losses are also described such as single exhaustive desorption and fractionated elutions for more detailed analyses. Documented results are also reported demonstrating the capability of the technology well beyond what is the common assumption.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
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31
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Doucette AA, Vieira DB, Orton DJ, Wall MJ. Resolubilization of precipitated intact membrane proteins with cold formic acid for analysis by mass spectrometry. J Proteome Res 2014; 13:6001-12. [PMID: 25384094 DOI: 10.1021/pr500864a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein precipitation in organic solvent is an effective strategy to deplete sodium dodecyl sulfate (SDS) ahead of MS analysis. Here we evaluate the recovery of membrane and water-soluble proteins through precipitation with chloroform/methanol/water or with acetone (80%). With each solvent system, membrane protein recovery was greater than 90%, which was generally higher than that of cytosolic proteins. With few exceptions, residual supernatant proteins detected by MS were also detected in the precipitation pellet, having higher MS signal intensity in the pellet fraction. Following precipitation, we present a novel strategy for the quantitative resolubilization of proteins in an MS-compatible solvent system. The pellet is incubated at -20 °C in 80% formic acid/water and then diluted 10-fold with water. Membrane protein recovery matches that of sonication of the pellet in 1% SDS. The resolubilized proteins are stable at room temperature, with no observed formylation as is typical of proteins suspended in formic acid at room temperature. The protocol is applied to the molecular weight determination of membrane proteins from a GELFrEE-fractionated sample of Escherichia coli proteins.
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Affiliation(s)
- Alan A Doucette
- Department of Chemistry and ‡Department of Pathology, Dalhousie University , Halifax, Nova Scotia, Canada
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32
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Lerma-García MJ, D’Amato A, Fasoli E, Simó-Alfonso EF, Righetti PG. According to the CPLL proteome sheriffs, not all aperitifs are created equal! BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1493-9. [DOI: 10.1016/j.bbapap.2014.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/24/2014] [Accepted: 04/28/2014] [Indexed: 12/01/2022]
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33
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Proteomics analysis for finding serum markers of ovarian cancer. BIOMED RESEARCH INTERNATIONAL 2014; 2014:179040. [PMID: 25250314 PMCID: PMC4164372 DOI: 10.1155/2014/179040] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/18/2014] [Indexed: 11/18/2022]
Abstract
A combination of peptide ligand library beads (PLLB) and 1D gel liquid chromatography-mass spectrometry/mass spectrometry (1DGel-LC-MS/MS) was employed to analyze serum samples from patients with ovarian cancer and from healthy controls. Proteomic analysis identified 1200 serum proteins, among which 57 proteins were upregulated and 10 were downregulated in the sera from cancer patients. Retinol binding protein 4 (RBP4) is highly upregulated in the ovarian cancer serum samples. ELISA was employed to measure plasma concentrations of RBP4 in 80 samples from ovarian cancer patients, healthy individuals, myoma patients, and patients with benign ovarian tumor, respectively. The plasma concentrations of RBP4 ranging from 76.91 to 120.08 ng/mL with the mean value 89.13 ± 1.67 ng/mL in ovarian cancer patients are significantly higher than those in healthy individuals (10.85 ± 2.38 ng/mL). Results were further confirmed with immunohistochemistry, demonstrating that RBP4 expression levels in normal ovarian tissue were lower than those in ovarian cancer tissues. Our results suggested that RBP4 is a potential biomarker for diagnostic of screening ovarian cancer.
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34
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Righetti PG, Candiano G, Citterio A, Boschetti E. Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics. Anal Chem 2014; 87:293-305. [DOI: 10.1021/ac502171b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
| | - Giovanni Candiano
- Laboratory on Pathophysiology of Uremia
and Department of Nephrology, Istituto Giannina Gaslini, Genova, Italy
| | - Attilio Citterio
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
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35
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From hundreds to thousands: Widening the normal human Urinome (1). J Proteomics 2014; 112:53-62. [PMID: 25123350 DOI: 10.1016/j.jprot.2014.07.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/22/2022]
Abstract
UNLABELLED It is currently unknown how many proteins can be detected in urine. Improving the analytical approach would increase their number and potentially strengthen their predictive potential in diseases. We developed a combination of analytical procedures for maximizing sensitivity and reproducibility of normal human urinary proteome analysis based on ultracentrifugation, vesicles separation, combinatorial peptide ligand libraries (CPLL) and solvent removal of pigments. Proteins were identified by an Orbitrap Velos Mass Spectrometry. Overall, 3429 proteins were characterized: most components (1615) were contained in vesicles while the remaining 1794 were equally distributed among CPLL and butanol insoluble fractions. Several proteins were detected exclusively in one of the phases of the procedure, suggesting that each step is crucial in the fractionation strategy. Many (1724) proteins are described here whose presence in urine has never been reported and represents a potential source of information considering that urine is the unique site of excretion of products of interaction of metabolic processes. Improving the characterization of normal urinary proteome would also represent the basis for the analysis of urine biomarkers in human diseases. BIOLOGICAL SIGNIFICANCE Sub-fractionating normal urine by successive steps (vesicle separation, CPLL and solvent treatments) allowed the identification of 3429 proteins, a relevant part (1724) being detected for the first time in urine. Several proteins of new description have been implicated in physiology pathways and in pathologies thus representing a potential source of new information on both metabolic processes and diseases.
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Abstract
The question of low-abundance proteins from biological tissues is still a major issue. Technologies have been devised to improve the situation and in the last few years a method based on solid-phase combinatorial peptide ligand libraries has been extensively applied to animal extracts. This method has also been extended to plant extracts taking advantage of findings from previous experience. Detailed methods are described and their pertinence highlighted according to various situations of plant sample origin, size of the sample, and analytical methods intended to be used for protein identifications.
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37
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Fasoli E, Righetti PG. The peel and pulp of mango fruit: A proteomic samba. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2539-45. [DOI: 10.1016/j.bbapap.2013.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/29/2013] [Accepted: 09/10/2013] [Indexed: 12/31/2022]
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38
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Esteve C, D'Amato A, Marina ML, García MC, Righetti PG. Analytical approaches for the characterization and identification of olive (Olea europaea) oil proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:10384-10391. [PMID: 24128378 DOI: 10.1021/jf4028359] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Proteins in olive oil have been scarcely investigated probably due to the difficulty of working with such a lipidic matrix and the dramatically low abundance of proteins in this biological material. Additionally, this scarce information has generated contradictory results, thus requiring further investigations. This work treats this subject from a comprehensive point of view and proposes the use of different analytical approaches to delve into the characterization and identification of proteins in olive oil. Different extraction methodologies, including capture via combinational hexapeptide ligand libraries (CPLLs), were tried. A sequence of methodologies, starting with off-gel isoelectric focusing (IEF) followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) or high-performance liquid chromatography (HPLC) using an ultraperformance liquid chromatography (UPLC) column, was applied to profile proteins from olive seed, pulp, and oil. Besides this, and for the first time, a tentative identification of oil proteins by mass spectrometry has been attempted.
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Affiliation(s)
- Clara Esteve
- Department of Analytical Chemistry, University of Alcalá , Carretera Madrid-Barcelona, Km. 33.600, E-28871 Alcalá de Henares, Madrid, Spain
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39
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Henning AK, Groschup MH, Mettenleiter TC, Karger A. Analysis of the bovine plasma proteome by matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry. Vet J 2013; 199:175-80. [PMID: 24268478 DOI: 10.1016/j.tvjl.2013.10.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 10/15/2013] [Accepted: 10/18/2013] [Indexed: 01/03/2023]
Abstract
In this study, the bovine plasma proteome was analysed using a three step protocol: (1) plasma was treated with a combinatorial peptide ligand library (CPLL) to assimilate the differences in concentrations of different proteins in raw plasma; (2) CPLL-treated material was fractionated by three standard electrophoretic separation techniques, and (3) samples were analysed by nano-liquid chromatography (nLC) matrix-assisted laser desorption/ionisation (MALDI) time-of-flight tandem (TOF/TOF) mass spectrometry. The efficiencies of three fractionation protocols for plasma proteome analysis were compared. After size fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), resolution of proteins was better and yields of identified proteins were higher than after charge-based fractionation by preparative gel-free isoelectric focussing. For proteins with isoelectric points >6 and molecular weights ⩾ 63 kDa, the best results were obtained with a 'shotgun' approach, in which the CPLL-treated plasma was digested and the peptides, rather than the proteins, were fractionated by gel-free isoelectric focussing. However, the three fractionation techniques were largely complementary, since only about one-third of the proteome was identified by each approach.
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Affiliation(s)
- Ann-Kristin Henning
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany; Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
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40
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Optimized sample treatment protocol by solid-phase peptide libraries to enrich for protein traces. Amino Acids 2013; 45:1431-42. [DOI: 10.1007/s00726-013-1596-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/12/2013] [Indexed: 12/11/2022]
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41
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Fasoli E, Colzani M, Aldini G, Citterio A, Righetti PG. Lemon peel and Limoncello liqueur: A proteomic duet. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1484-91. [DOI: 10.1016/j.bbapap.2013.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/23/2022]
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42
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Černý M, Skalák J, Cerna H, Brzobohatý B. Advances in purification and separation of posttranslationally modified proteins. J Proteomics 2013; 92:2-27. [PMID: 23777897 DOI: 10.1016/j.jprot.2013.05.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 11/25/2022]
Abstract
Posttranslational modifications (PTMs) of proteins represent fascinating extensions of the dynamic complexity of living cells' proteomes. The results of enzymatically catalyzed or spontaneous chemical reactions, PTMs form a fourth tier in the gene - transcript - protein cascade, and contribute not only to proteins' biological functions, but also to challenges in their analysis. There have been tremendous advances in proteomics during the last decade. Identification and mapping of PTMs in proteins have improved dramatically, mainly due to constant increases in the sensitivity, speed, accuracy and resolution of mass spectrometry (MS). However, it is also becoming increasingly evident that simple gel-free shotgun MS profiling is unlikely to suffice for comprehensive detection and characterization of proteins and/or protein modifications present in low amounts. Here, we review current approaches for enriching and separating posttranslationally modified proteins, and their MS-independent detection. First, we discuss general approaches for proteome separation, fractionation and enrichment. We then consider the commonest forms of PTMs (phosphorylation, glycosylation and glycation, lipidation, methylation, acetylation, deamidation, ubiquitination and various redox modifications), and the best available methods for detecting and purifying proteins carrying these PTMs. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Martin Černý
- Department of Molecular Biology and Radiobiology, Mendel University in Brno & CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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D'Amato A, Esteve C, Fasoli E, Citterio A, Righetti PG. Proteomic analysis ofLycium barbarum(Goji) fruit via combinatorial peptide ligand libraries. Electrophoresis 2013. [DOI: 10.1002/elps.201200643] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alfonsina D'Amato
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
| | - Clara Esteve
- Department of Analytical Chemistry; Faculty of Chemistry; University of Alcalá; Alcalá de Henares; Madrid; Spain
| | - Elisa Fasoli
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
| | - Attilio Citterio
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
| | - Pier Giorgio Righetti
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
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Combinatorial ligand libraries as a two-dimensional method for proteome analysis. J Chromatogr A 2013; 1297:106-12. [PMID: 23726082 DOI: 10.1016/j.chroma.2013.04.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/19/2013] [Accepted: 04/23/2013] [Indexed: 12/17/2022]
Abstract
The present report tries to assess the possibility of performing capture of proteomes via combinatorial peptide ligand libraries (CPLL) in a two-dimensional (2D) mode, i.e. via orthogonal complementarity in the capture phase. To that aim, serum proteins are captured at physiological pH either at low ionic strength (25mM NaCl) or at high concentrations of lyotropic salts of the Hofmeister series (1M ammonium sulphate) favouring hydrophobic interaction. Indeed such 2D mechanisms seems to be operative, since 52% of the captured proteins are common to the two capture modes, 20% are specific only of the "ionic" interaction mode and 28% are found only in the "hydrophobically" driven interaction. As an additional bonus, losses of protein species from the initial sample, one of the major drawbacks of CPLLs, are diminished to about 5% and are found only in the ionic capture, whereas the hydrophobically engendered capture is loss-free.
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Artichoke and Cynar liqueur: Two (not quite) entangled proteomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:119-26. [DOI: 10.1016/j.bbapap.2012.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 01/13/2023]
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46
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Battiston KG, Labow RS, Santerre JP. Protein binding mediation of biomaterial-dependent monocyte activation on a degradable polar hydrophobic ionic polyurethane. Biomaterials 2012; 33:8316-28. [DOI: 10.1016/j.biomaterials.2012.08.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 08/05/2012] [Indexed: 12/25/2022]
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47
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Righetti PG, Boschetti E, Candiano G. Mark Twain: How to fathom the depth of your pet proteome. J Proteomics 2012; 75:4783-91. [DOI: 10.1016/j.jprot.2012.05.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 05/28/2012] [Accepted: 05/30/2012] [Indexed: 02/06/2023]
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48
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Assessment of the floral origin of honey via proteomic tools. J Proteomics 2012; 75:3688-93. [DOI: 10.1016/j.jprot.2012.04.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/20/2012] [Accepted: 04/21/2012] [Indexed: 11/19/2022]
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49
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Fasoli E, D'Amato A, Citterio A, Righetti PG. Anyone for an aperitif? Yes, but only a Braulio DOC with its certified proteome. J Proteomics 2012; 75:3374-9. [DOI: 10.1016/j.jprot.2012.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/12/2012] [Accepted: 04/16/2012] [Indexed: 12/25/2022]
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50
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Fasoli E, D'Amato A, Righetti PG, Barbieri R, Bellavia D. Exploration of the sea urchin coelomic fluid via combinatorial peptide ligand libraries. THE BIOLOGICAL BULLETIN 2012; 222:93-104. [PMID: 22589400 DOI: 10.1086/bblv222n2p93] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The urchin Paracentrotus lividus has been characterized via previous capture and enhancement of low-abundance proteins with combinatorial peptide ligand libraries (CPLL, ProteoMiner). Whereas in the control only 26 unique gene products could be identified, 82 species could be detected after CPLL treatment. Due to the overwhelming presence of two major proteins-the toposome (a highly glycosylated, modified calcium-binding, iron-less transferrin) and the major yolk proteins, belonging to the class of cell adhesion proteins-which constituted about 70% of the proteome of this biological fluid and strongly interfered with the capture of the minority proteome, no additional proteins could be detected. Yet, at present, this constitutes the most thorough investigation of the proteome of this biological fluid.
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Affiliation(s)
- Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Politecnico di Milano, Via Mancinelli 7, Milan, Italy
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