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Article ; Online: Differential Proteomic Analysis of Complex Mixtures by Label-Free nLC MS/MS.

Escobés, Iraide / Azkargorta, Mikel / Iloro, Ibon / Elortza, Felix

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2471, Page(s) 111–121

Abstract: After over two decades of constant evolution, proteomics can be truly considered nowadays as a high-throughput technique. Latest advances performed in sample preparation, instrumentation, and data analysis tools enable proteome-wide detection and ... ...

Abstract	After over two decades of constant evolution, proteomics can be truly considered nowadays as a high-throughput technique. Latest advances performed in sample preparation, instrumentation, and data analysis tools enable proteome-wide detection and quantification of proteins in complex samples.Label-free quantification by nanoscale liquid chromatography coupled online to tandem mass spectrometry (nLC MS /MS ) is a straightforward procedure for relative protein quantification. This approach allows to get deeper insights of what molecular changes are involved in the biological system we want to study in an unbiased manner.This chapter describes methods for sample preparation prior to mass spectrometry analysis. Besides, we describe a standard acquisition method, and some common bioinformatics analyses that help extracting biologically relevant information out of the achieved data.
MeSH term(s)	Chromatography, Liquid/methods ; Complex Mixtures ; Proteome/analysis ; Proteomics/methods ; Tandem Mass Spectrometry/methods
Chemical Substances	Complex Mixtures ; Proteome
Language	English
Publishing date	2022-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2193-6_5
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Article: Müller glial cells located in the peripheral retina are more susceptible to high pressure: implications for glaucoma.

Pereiro, Xandra / Ruzafa, Noelia / Azkargorta, Mikel / Elortza, Félix / Acera, Arantxa / Ambrósio, António Francisco / Santiago, Ana Raquel / Vecino, Elena

Cell & bioscience

2024 Volume 14, Issue 1, Page(s) 5

Abstract: Background: Glaucoma, a progressive neurodegenerative disease, is a leading cause of irreversible vision loss worldwide. This study aims to elucidate the critical role of Müller glia (MG) in the context of retinal ganglion cell (RGC) death, particularly ...

Abstract	Background: Glaucoma, a progressive neurodegenerative disease, is a leading cause of irreversible vision loss worldwide. This study aims to elucidate the critical role of Müller glia (MG) in the context of retinal ganglion cell (RGC) death, particularly focusing on the influence of peripheral MG sensitivity to high pressure (HP). Methods: Co-cultures of porcine RGCs with MG were isolated from both the central and peripheral regions of pig retinas and subjected to both normal and HP conditions. Mass spectrometry analysis of the MG-conditioned medium was conducted to identify the proteins released by MG under all conditions. Results: Peripheral MG were found to secrete a higher quantity of neuroprotective factors, effectively promoting RGC survival under normal physiological conditions. However, under HP conditions, co-cultures with peripheral MG exhibited impaired RGC survival. Moreover, under HP conditions, peripheral MG significantly upregulated the secretion of proteins associated with apoptosis, oxidative stress, and inflammation. Conclusions: This study provides robust evidence suggesting the involvement of MG in RGC death in glaucoma, thus paving the way for future therapeutic investigations.
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2593367-X
ISSN	2045-3701
ISSN	2045-3701
DOI	10.1186/s13578-023-01186-1
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Article ; Online: High-Throughput Proteomic Analysis of Human Dermal Fibroblast Response to Different Blood Derivatives: Autologous Topical Serum Derived from Plasma Rich in Growth Factors (PRGF) versus Leukocyte- and Platelet-Rich Plasma (L-PRP).

Anitua, Eduardo / Pino, Ander / Azkargorta, Mikel / Elortza, Felix / Prado, Roberto

Biomolecules

2022 Volume 12, Issue 7

Abstract: Platelet-rich plasma (PRP) is nowadays used in the treatment of different types of cutaneous lesions. However, different compositions can influence clinical outcomes. Among them, the inclusion of leukocytes is controversial. High-throughput proteomics ... ...

Abstract	Platelet-rich plasma (PRP) is nowadays used in the treatment of different types of cutaneous lesions. However, different compositions can influence clinical outcomes. Among them, the inclusion of leukocytes is controversial. High-throughput proteomics techniques were used to analyze the proteins that are differentially expressed in human dermal fibroblasts (HDFs) after treatment for 24 h with two PRP types, autologous topical serum (Endoret serum-ES) derived from plasma rich in growth factors (PRGF) and leukocyte- and platelet-rich plasma (L-PRP). The identified proteins were then classified by both Gene Ontology and Ingenuity Pathway Analysis. The obtained results show that the compositions of ES and L-PRP differ in such a way that they induce different responses in HDFs. ES-treated HDFs overexpress growth factor-related proteins, leading to protein synthesis, cell proliferation and migration. By contrast, L-PRP treatment induces a response similar to that caused by proinflammatory molecules. These data could explain the contradictory clinical results obtained for the different types of PRP, especially with respect to their leukocyte contents.
MeSH term(s)	Fibroblasts ; Humans ; Intercellular Signaling Peptides and Proteins/metabolism ; Leukocytes/metabolism ; Platelet-Rich Plasma/metabolism ; Proteomics
Chemical Substances	Intercellular Signaling Peptides and Proteins
Language	English
Publishing date	2022-07-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12071002
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Article ; Online: Comparative proteomic analysis of the changes in mare milk associated with different lactation stages and management systems.

Blanco-Doval, Ana / Azkargorta, Mikel / Iloro, Ibon / Beaskoetxea, Jabier / Elortza, Felix / Barron, Luis Javier R / Aldai, Noelia

Food chemistry

2024 Volume 445, Page(s) 138766

Abstract: Mare milk has traditionally been attributed a number of health promoting properties. However, knowledge on its composition and functionality remains scarce, with particularly limited studies on mare milk proteomics. This study deeply characterized mare ... ...

Abstract	Mare milk has traditionally been attributed a number of health promoting properties. However, knowledge on its composition and functionality remains scarce, with particularly limited studies on mare milk proteomics. This study deeply characterized mare milk proteome accounting for both caseins and proteins in the whey fraction, also addressing the impact of lactation stage and different management systems. Milk samples from Basque Mountain Horse breed mares belonging to three different farms and three lactation stages were analysed after in-gel and in-solution digestion using nLC-MS/MS. Among the 469 proteins identified, the content of alpha-1 antitrypsin was significantly higher in pasture-based compared to other systems. Moreover, lactation stage significantly affected the content of beta-lactoglobulin II, immunoglobulin-like domain-containing protein, interferon alpha-inducible protein 27, lactotransferrin, polypeptide N-acetylgalactosaminyltransferase, and transforming acidic coiled-coil containing protein 2. This study contributes to the deep characterization of mare milk proteome and provides new insights into the effect of different production factors.
MeSH term(s)	Horses ; Animals ; Female ; Milk/chemistry ; Milk Proteins/analysis ; Tandem Mass Spectrometry ; Proteome/analysis ; Proteomics ; Lactation
Chemical Substances	Milk Proteins ; Proteome
Language	English
Publishing date	2024-02-17
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2024.138766
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Article ; Online: Molecular Histology Analysis of Cryopreserved Tissue Using Peptide/Protein MALDI-TOF Imaging Mass Spectrometry (MALDI-IMS).

Iloro, Ibon / Escobés, Iraide / Azkargorta, Mikel / Elortza, Félix

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2420, Page(s) 177–190

Abstract: Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) has emerged as a powerful tool for analyzing the spatial distribution of peptides, small proteins, and other molecules within biological tissues. The obtained signals can ...

Abstract	Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) has emerged as a powerful tool for analyzing the spatial distribution of peptides, small proteins, and other molecules within biological tissues. The obtained signals can be correlated with underlying tissue architecture, without any geometrical distortion, enabling the so-called molecular histology. Here, we analyzed cryopreserved tissue samples employing the MALDI-IMS for proteins and peptides. We used a nonstandard OCT-free cryo-slicing protocol, followed by Carnoy delipidation. Automated matrix spray was utilized to circumvent some of MALDI-IMS technology drawbacks in protein and peptide analysis.
MeSH term(s)	Histological Techniques ; Molecular Imaging ; Peptides ; Proteins ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	Peptides ; Proteins
Language	English
Publishing date	2021-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1936-0_14
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Differential Protein Content between Fresh and Freeze-Dried Plasma Rich in Growth Factors Eye Drops.

Anitua, Eduardo / Pino, Ander / Azkargorta, Mikel / Elortza, Felix / Merayo-Lloves, Jesús / Muruzabal, Francisco

Biomolecules

2022 Volume 12, Issue 9

Abstract: The purpose of this study was to analyze the proteomic composition of plasma rich in growth factors eye drops (PRGF) in comparison to lyophilized PRGF eye drops (PRGF lyo). The differential protein expression of keratocyte (HK) cells after PRGF or PRGF ... ...

Abstract	The purpose of this study was to analyze the proteomic composition of plasma rich in growth factors eye drops (PRGF) in comparison to lyophilized PRGF eye drops (PRGF lyo). The differential protein expression of keratocyte (HK) cells after PRGF or PRGF lyo treatment was also determined. Blood from different donors was collected and processed to obtain PRGF and PRGF lyo eye drops. Then, HK cells were treated with both formulations. A proteomic analysis was performed to evaluate the differential proteomic profile between PRGF and PRGF lyo, and the differential protein expression by HK cells after treatment with both blood-derived products. About 280 proteins were detected between both blood-derived formulation, with only 8 of them reaching significant differences. Furthermore, 101 out of 3213 proteins showed statistically significant deregulation in HK cells after treatment with PRGF or PRGF lyo. Gene Ontology analysis showed that these significant deregulated proteins were involved in 30 functional processes. However, the Ingenuity Pathway Analysis showed that no significant differences were found in any of the identified processes. In summary, the present study show that no significant differences were found in the proteomic profile or in the signaling pathways activation in HK cells between PRGF and PRGF lyo.
MeSH term(s)	Intercellular Signaling Peptides and Proteins ; Ophthalmic Solutions/pharmacology ; Plasma ; Proteomics
Chemical Substances	Intercellular Signaling Peptides and Proteins ; Ophthalmic Solutions
Language	English
Publishing date	2022-09-01
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12091215
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Article: A Three-Protein Panel to Support the Diagnosis of Sepsis in Children.

Pilar-Orive, Francisco J / Astigarraga, Itziar / Azkargorta, Mikel / Elortza, Felix / Garcia-Obregon, Susana

Journal of clinical medicine

2022 Volume 11, Issue 6

Abstract: Sepsis is a syndrome without a standard validated diagnostic test. Early recognition is crucial. Serum proteome analysis in children with sepsis may identify new biomarkers. This study aimed to find suitable blood biomarkers for an early diagnosis of ... ...

Abstract	Sepsis is a syndrome without a standard validated diagnostic test. Early recognition is crucial. Serum proteome analysis in children with sepsis may identify new biomarkers. This study aimed to find suitable blood biomarkers for an early diagnosis of sepsis. An analytical observational case-control study was carried out in a single center. Children admitted to a Pediatric Intensive Care Unit with clinical diagnosed sepsis were eligible for study. A proteomic analysis conducted by mass spectrometry was performed. Forty patients with sepsis and 24 healthy donors were recruited. Proteomics results revealed 44 proteins differentially expressed between patients and healthy controls. Six proteins were selected to be validated: lactoferrin, serum amyloid-A1 (SAA-1), complement factor B, leucine-rich alpha-2 glycoprotein (LRG1), soluble interleukin-2 alpha chain receptor (sCD25) and soluble haptoglobin−hemoglobin receptor. Our results showed that sCD25, SAA-1, and LRG1 had high levels of specificity and sensitivity, as well as an excellent area under the ROC curve (>0.9). Our study provides a serum proteomic analysis that identifies new diagnostic biomarkers in sepsis. SAA-1, sCD25 and LRG1 were able to separate septic from healthy donor, so they could be used together with other clinical and analytical features to improve sepsis diagnosis in children.
Language	English
Publishing date	2022-03-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm11061563
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Article ; Online: Proteomics as a tool to study the osteoimmunomodulatory role of metallic ions in a sol-gel coating.

García-Arnáez, Iñaki / Romero-Gavilán, Francisco / Cerqueira, Andreia / Azkargorta, Mikel / Elortza, Félix / Suay, Julio / Goñi, Isabel / Gurruchaga, Mariló

Journal of materials chemistry. B

2023 Volume 11, Issue 34, Page(s) 8194–8205

Abstract: The success of bone implants depends on the osteoimmunomodulatory (OIM) activity of the biomaterials in the interactions with the periimplantary tissues. ... ...

Abstract	The success of bone implants depends on the osteoimmunomodulatory (OIM) activity of the biomaterials in the interactions with the periimplantary tissues. Many
MeSH term(s)	Coated Materials, Biocompatible/pharmacology ; Proteomics ; Metals ; Bone Regeneration ; Ions
Chemical Substances	Coated Materials, Biocompatible ; Metals ; Ions
Language	English
Publishing date	2023-08-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2702241-9
ISSN	2050-7518 ; 2050-750X
ISSN (online)	2050-7518
ISSN	2050-750X
DOI	10.1039/d3tb01204b
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Article ; Online: Region-Directed Enzyme Immobilization through Engineering Protein Surface with Histidine Clusters.

Zeballos, Nicoll / Comino, Natalia / Andrés-Sanz, Daniel / Santiago-Arcos, Javier / Azkargorta, Mikel / Elortza, Felix / Diamanti, Eleftheria / López-Gallego, Fernando

ACS applied materials & interfaces

2023 Volume 16, Issue 1, Page(s) 833–846

Abstract: Enzyme immobilization is a key enabling technology for a myriad of industrial applications, yet immobilization science is still too empirical to reach highly active and robust heterogeneous biocatalysts through a general approach. Conventional protein ... ...

Abstract	Enzyme immobilization is a key enabling technology for a myriad of industrial applications, yet immobilization science is still too empirical to reach highly active and robust heterogeneous biocatalysts through a general approach. Conventional protein immobilization methods lack control over how enzymes are oriented on solid carriers, resulting in negative conformational changes that drive enzyme deactivation. Site-selective enzyme immobilization through peptide tags and protein domains addresses the orientation issue, but this approach limits the possible orientations to the N- and C-termini of the target enzyme. In this work, we engineer the surface of two model dehydrogenases to introduce histidine clusters into flexible regions not involved in catalysis, through which immobilization is driven. By varying the position and the histidine density of the clusters, we create a small library of enzyme variants to be immobilized on different carriers functionalized with different densities of various metal chelates (Co
MeSH term(s)	Enzymes, Immobilized/chemistry ; Histidine/chemistry ; Proteomics ; Protein Engineering ; Metals ; Membrane Proteins
Chemical Substances	Enzymes, Immobilized ; Histidine (4QD397987E) ; Metals ; Membrane Proteins
Language	English
Publishing date	2023-12-22
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c15993
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Article ; Online: Proteomic Analysis of Mesenchymal Stem Cells and Monocyte Co-Cultures Exposed to a Bioactive Silica-Based Sol-Gel Coating.

Cerqueira, Andreia / Romero-Gavilán, Francisco / Helmholz, Heike / Azkargorta, Mikel / Elortza, Félix / Gurruchaga, Mariló / Goñi, Isabel / Willumeit-Römer, Regine / Suay, Julio

ACS biomaterials science & engineering

2023 Volume 9, Issue 6, Page(s) 3306–3319

Abstract: New methodologies capable of extensively analyzing the cell-material interactions are necessary to improve current in vitro characterization methods, and proteomics is a viable alternative. Also, many studies are focused on monocultures, even though co- ... ...

Abstract	New methodologies capable of extensively analyzing the cell-material interactions are necessary to improve current in vitro characterization methods, and proteomics is a viable alternative. Also, many studies are focused on monocultures, even though co-cultures model better the natural tissue. For instance, human mesenchymal stem cells (MSCs) modulate immune responses and promote bone repair through interaction with other cell types. Here, label-free liquid chromatography tandem mass spectroscopy proteomic methods were applied for the first time to characterize HUCPV (MSC) and CD14
MeSH term(s)	Humans ; Monocytes ; Coculture Techniques ; Proteomics ; Mesenchymal Stem Cells/metabolism ; Integrins/metabolism ; Silicon Dioxide/chemistry ; Silicon Dioxide/metabolism ; Glutathione Transferase/metabolism
Chemical Substances	Integrins ; Silicon Dioxide (7631-86-9) ; GSTO1 protein, human (EC 2.5.1.18) ; Glutathione Transferase (EC 2.5.1.18)
Language	English
Publishing date	2023-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2373-9878
ISSN (online)	2373-9878
DOI	10.1021/acsbiomaterials.3c00254
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