Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics.

Over the last two decades, EDTA-plasma has been used as the preferred sample matrix for human blood proteomic profiling. Serum has also been employed widely. Only a few studies have assessed the difference and relevance of the proteome profiles obtained from plasma samples, such as EDTA-plasma or lithium-heparin-plasma, and serum. A more complete evaluation of the use of EDTA-plasma, heparin-plasma, and serum would greatly expand the comprehensiveness of shotgun proteomics of blood samples. In this study, we evaluated the use of heparin-plasma with respect to EDTA-plasma and serum to profile blood proteomes using a scalable automated proteomic pipeline (ASAP2). The use of plasma and serum for mass-spectrometry-based shotgun proteomics was first tested with commercial pooled samples. The proteome coverage consistency and the quantitative performance were compared. Furthermore, protein measurements in EDTA-plasma and heparin-plasma samples were comparatively studied using matched sample pairs from 20 individuals from the Australian Imaging, Biomarkers and Lifestyle (AIBL) Study. We identified 442 proteins in common between EDTA-plasma and heparin-plasma samples. Overall agreement of the relative protein quantification between the sample pairs demonstrated that shotgun proteomics using workflows such as the ASAP2 is suitable in analyzing heparin-plasma and that such sample type may be considered in large-scale clinical research studies. Moreover, the partial proteome coverage overlaps (e.g., ∼70%) showed that measures from heparin-plasma could be complementary to those obtained from EDTA-plasma.

Efecto de dosis suprafisiológicas de calcitriol sobre la expresión proteica de células de músculo liso vascular / Effect of supra-physiological calcitriol doses on protein expression of vascular smooth muscle cells

Introducción: El calcitriol, fundamental para mantener la homeostasis del calcio y el fósforo en el organismo, puede perjudicar al sistema vascular a dosis elevadas, aumentando el riesgo de calcificación. Objetivo: Evaluar la expresión diferencial de proteínas en células de músculo liso vascular sometidas a una dosis suprafisiológica de calcitriol. Material y métodos: Se cultivaron células de músculo liso vascular de rata (SMAC-R) en presencia de 10-7 M de calcitriol durante 10 días. Se valoró el cambio de fenotipo muscular a óseo mediante actividad fosfatasa alcalina, inmunocitoquímica, reacción en cadena de la polimerasa cuantitativa a tiempo real (qPCR) y Western blot. Mediante electroforesis bidimensional y espectrometría de masas se evaluó el patrón diferencial de proteínas en presencia y ausencia de 10-7 M de calcitriol. Resultados: La exposición a una dosis alta de calcitriol disminuyó significativamente la expresión génica de elastina y la expresión génica y proteica de α-actina, aumentado la expresión génica de osteocalcina y Runx2 y la proteica de osteoprotegerina. A nivel proteómico se identificaron 10 proteínas diferencialmente expresadas, destacando el aumento en superóxido dismutasa mitocondrial, proteínas del citoesqueleto, de formación de vesículas y del inflamasoma. Por el contrario, hubo 4 proteínas que disminuyeron su expresión, destacando alguna de tipo muscular. Conclusiones: En un modelo de células de músculo liso vascular sometidas a una dosis suprafisiológica de calcitriol se observó un aumento de expresión de proteínas del citoesqueleto, que forman vesículas de matriz y que participan en depurar radicales libres y en la respuesta inflamatoria. La pérdida de fenotipo muscular se vio representada por descensos en la expresión de proteínas típicamente musculares (AU)

Introduction: Calcitriol, essential for maintaining calcium and phosphorus homeostasis in the body, may damage the vascular system in high doses, increasing the risk of calcification. Objective: To assess the differential expression of proteins in vascular smooth muscle cells subjected to a supra-physiological dose of calcitriol. Material and methods: Rat vascular smooth muscle cells (VSMC-R) were cultured in the presence of 10-7 M calcitriol for 10 days. The change of muscle to bone phenotype was assessed by alkaline phosphatase activity, immunocytochemistry, quantitative polymerase chain reaction in time (QPCR) and Western blot analysis. By means of two-dimensional electrophoresis and mass spectrometry was evaluated for the differential protein pattern in presence and absence of 10-7 M calcitriol. Results: Exposure to a high dose of calcitriol decreased elastin gene expression and the protein and gene expression of α-actin protein, increased gene expression of osteocalcin and Runx2 and expression of osteoprotegerin protein. At the proteomic level, 10 differentially expressed proteins were identified, highlighting the increase in mitochondrial superoxide dismutase, cytoskeleton proteins, vesicle formation and inflammasome. On the contrary, there were 4 proteins that diminished expression, highlighting some of muscular type. Conclusions: In a model of vascular smooth muscle cells submitted to a supra-physiological dose of calcitriol an increased expression of cytoskeleton proteins was observed. These proteins form matrix vesicles and participate in clearance of free radicals and in the inflammatory response. The loss of muscle phenotype was represented by decreased expression of typically muscle proteins (AU)

Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells.

We evaluated different in-solution and FASP-based sample preparation strategies for absolute protein quantification. Label-free quantification (LFQ) was employed to compare different sample preparation strategies in the bacterium Pseudomonas aeruginosa and human embryonic kidney cells (HEK), and organismal-specific differences in general performance and enrichment of specific protein classes were noted. The original FASP protocol globally enriched for most proteins in the bacterial sample, whereas the sodium deoxycholate in-solution strategy was more efficient with HEK cells. Although detergents were found to be highly suited for global proteome analysis, higher intensities were obtained for high-abundant nucleic acid-associated protein complexes, like the ribosome and histone proteins, using guanidine hydrochloride. Importantly, we show for the first time that the observable total proteome mass of a sample strongly depends on the sample preparation protocol, with some protocols resulting in a significant underestimation of protein mass due to incomplete protein extraction of biased protein groups. Furthermore, we demonstrate that some of the observed abundance biases can be overcome by incorporating a nuclease treatment step or, alternatively, a correction factor for complementary sample preparation approaches.

Antibodies: The generation game.

Proteomics is hungry for well-validated antibodies. Nathan Blow looks at the options and sees how researchers are redefining the way to generate an antibody.