Proteomic Stability and Ex Vivo Compatibility of a Processed Phospholipoproteic Secretome-Derived Formulation
Abstract
1. Introduction
2. Materials and Methods
2.1. Preparation of the Processed Phospholipoproteic Secretome-Derived Formulation
2.2. Processing Conditions
2.3. Proteomic Characterization
2.4. Short-Term Real-Time Live-Cell Kinetic Profiling
2.5. Data Integration and Quality Control
2.6. Statistical Analysis
2.7. Quality Control and Acceptance Criteria
3. Results
3.1. Proteomic Fingerprint and Structural Protein Conservation
3.2. Short-Term Real-Time Kinetic Profiling and Ex Vivo Compatibility
3.3. Functional Annotation of Processing-Associated Proteomic Changes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
| Abbreviation | Full Term |
| CTRL | Fresh control formulation |
| CRIO | Cryopreserved formulation |
| FILT | Concentrated formulation |
| LIOF | Lyophilized formulation |
| LFQ | Label-Free Quantification |
| DEP | Differentially Expressed Protein |
| CV | Coefficient of Variation |
| PCA | Principal Component Analysis |
| FDR | False Discovery Rate |
| dia-PASEF | Data-Independent Acquisition Parallel Accumulation–Serial Fragmentation |
| timsTOF Pro | Trapped Ion Mobility Spectrometry Time-of-Flight Pro mass spectrometer |
| SD | Standard Deviation |
| Lo | Liquid-Ordered phase |
| Ld | Liquid-Disordered phase |
| IncuCyte® S3 | Real-time live-cell kinetic imaging system |
| UniProt | Universal Protein Resource database |
| ANOVA | Analysis of Variance |
| Z-score | Standardized score normalization metric |
| PC1 | Principal Component 1 |
| PC2 | Principal Component 2 |
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| Component | Functional Role | Relative Proportion |
|---|---|---|
| Phospholipid-associated fraction | Membrane-associated structural organization | Predominant |
| Membrane-associated proteins | Structural and extracellular compatibility | Conserved proteomic fraction |
| Extracellular structural proteins | Organization of extracellular lipid–protein assemblies | Moderate abundance |
| Cytoskeletal-associated proteins | Structural compatibility and membrane-associated interactions | Trace–moderate abundance |
| Apolipoprotein-associated components | Lipid-associated stabilization | Trace abundance |
| Annexin-associated proteins | Membrane interaction and phospholipid-binding functions | Trace abundance |
| Extracellular matrix-associated proteins | Structural extracellular organization | Variable abundance |
| Parameter | Fresh (Reference) | Concentrated | Cryopreserved | Lyophilized |
|---|---|---|---|---|
| Total proteins identified | 574 | 562 | 545 | 533 |
| Structural protein retention | 100% | >92% | >91% | >90% |
| Mean coefficient of variation (CV) | 3.1% | 3.3% | 3.0% | 4.5% |
| Inter-replicate Pearson correlation | >0.97 | >0.97 | >0.96 | >0.95 |
| Differentially expressed proteins (DEPs) vs. fresh reference | — | 68 | 49 | 129 |
| Global proteomic profile conservation: | Reference profile | Preserved | Preserved | Partially preserved |
| LFQ reproducibility | High | High | High | High |
| Parameter | Vehicle Control | Fresh | Concentrated | Cryopreserved | Lyophilized |
|---|---|---|---|---|---|
| Cell viability at 48 h | 100 ± 5% | 98 ± 7% | 98 ± 6% | 97 ± 6% | 96 ± 7% |
| Maximum confluence divergence from vehicle | — | <5% | <5% | <6% | <7% |
| Mean intra-experimental CV | <10% | <9% | <9% | <8% | <10% |
| Morphological alterations | None detected | None detected | None detected | None detected | None detected |
| Evidence of blebbing | Absent | Absent | Absent | Absent | Absent |
| Evidence of detachment | Absent | Absent | Absent | Absent | Absent |
| Evidence of proliferative suppression | Absent | Absent | Absent | Absent | Absent |
| Overall kinetic compatibility | Reference profile | Preserved | Preserved | Preserved | Preserved |
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Gutiérrez-Sandoval, R.; Gutiérrez-Castro, F.; Muñoz-Godoy, N.; Rivadeneira, I.; Lagos, A.; Iturra, J.; Krakowiak, F.; Muñoz, I.; Toledo, A. Proteomic Stability and Ex Vivo Compatibility of a Processed Phospholipoproteic Secretome-Derived Formulation. Pharmaceutics 2026, 18, 847. https://doi.org/10.3390/pharmaceutics18070847
Gutiérrez-Sandoval R, Gutiérrez-Castro F, Muñoz-Godoy N, Rivadeneira I, Lagos A, Iturra J, Krakowiak F, Muñoz I, Toledo A. Proteomic Stability and Ex Vivo Compatibility of a Processed Phospholipoproteic Secretome-Derived Formulation. Pharmaceutics. 2026; 18(7):847. https://doi.org/10.3390/pharmaceutics18070847
Chicago/Turabian StyleGutiérrez-Sandoval, Ramón, Francisco Gutiérrez-Castro, Natalia Muñoz-Godoy, Ider Rivadeneira, Andy Lagos, Jordan Iturra, Francisco Krakowiak, Ignacio Muñoz, and Andrés Toledo. 2026. "Proteomic Stability and Ex Vivo Compatibility of a Processed Phospholipoproteic Secretome-Derived Formulation" Pharmaceutics 18, no. 7: 847. https://doi.org/10.3390/pharmaceutics18070847
APA StyleGutiérrez-Sandoval, R., Gutiérrez-Castro, F., Muñoz-Godoy, N., Rivadeneira, I., Lagos, A., Iturra, J., Krakowiak, F., Muñoz, I., & Toledo, A. (2026). Proteomic Stability and Ex Vivo Compatibility of a Processed Phospholipoproteic Secretome-Derived Formulation. Pharmaceutics, 18(7), 847. https://doi.org/10.3390/pharmaceutics18070847

