Principal component analysis on LC‑MS/MS and 2DE‑MALDI‑TOF in glioblastoma cell lines reveals that mitochondria act as organelle sensors of the metabolic state in glioblastoma

Abstract

Glioblastoma is a difficult disease to diagnose. Proteomic techniques are commonly applied in biomedical research, and can be useful for early detection, making an accurate diagnosis and reducing mortality. The relevance of mitochondria in brain development and function is well known; therefore, mitochondria may influence the development of glioblastoma. The T98G (with oxidative metabolism) and U87MG (with glycolytic metabolism) cell lines are considered to be useful glioblastoma models for studying these tumors and the role of mitochondria in key aspects of this disease, such as prognosis, metastasis and apoptosis. In the present study, principal component analysis of protein abundance data identified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF) from 2D gels indicated that representative mitochondrial proteins were associated with glioblastoma. The selected proteins were organized into T98G-and U87MG-specific protein-protein interaction networks to demonstrate the representativeness of both proteomic techniques. Gene Ontology overrepresentation analysis based on the relevant proteins revealed that mitochondrial processes were associated with metabolic changes, invasion and metastasis in glioblastoma, along with other non-mitochondrial processes, such as DNA translation, chaperone responses and autophagy. Despite the lower resolution of 2D electrophoresis, principal component analysis yielded information of comparable quality to that of LC-MS/MS. The present analysis pipeline described a specific and more complete metabolic status for each cell line, defined a clear mitochondrial performance for distinct glioblastoma tumors, and introduced a useful strategy to understand the heterogeneity of glioblastoma.

The Differential Metabolomes in Cumulus and Mural Granulosa Cells from Human Preovulatory Follicles

“…Ion source gas1 (Gas1) was set to 60, gas2 was also 60, and curtain gas (CUR) was 30. Ion spray voltage floating (ISVF) was ±5500 V (positive and negative modes); the source temperature was 600°C; the m/z range of TOF MS scan and product ion scan was 60-1000 Da and 25-1000 Da, respectively; the accumulation time of TOF MS scan and product ion scan was 0.20 s/spectra and 0.05 s/spectra, respectively; the secondary mass spectra were obtained by informationdependent acquisition (IDA); high sensitivity mode was adopted; the declustering potential (DP) was set to ±60 V (positive and negative modes); the collision energy was 35 ± 15 eV; the IDA setting excluded isotopes within 4 Da; and the candidate ions to monitor per cycle was 6 [21][22][23].…”

Dysregulated sphingolipid metabolism and autophagy in granulosa cells of women with endometriosis

“…IonSapary Voltage Floating (ISVF) was ±5,500 V (positive and negative modes); source temperature was 600°C; the m / z range of time-of-flight (TOF) MS scan and product ion scan was 60–1,000 and 25–1,000 Da, respectively; the accumulation time of TOF MS scan and product ion scan were 0.20 s/spectra and 0.05 s/spectra, respectively; the secondary mass spectrum was obtained by information-dependent acquisition (IDA) and adopts high sensitivity mode; declustering potential (DP) was set to ±60 V (positive and negative modes); collision energy was 35 ± 15 eV. IDA setting excludes isotopes within 4 Da, with candidate ions to monitor per cycle of 6 ( 24 – 26 ).…”

Expression Profiles of Kidney Mitochondrial Proteome during the Progression of the Unilateral Ureteral Obstruction: Focus on Energy Metabolism Adaptions

“…The process used for the statistical analysis of the proteomic data was based on the methodology described previously [ 26 ] with some modifications. In the first part of our analysis, all identified and quantified proteins were checked for mitochondrial protein selection against a list of mitochondrial or mitochondrial traffic proteins reported by MitoMiner [ 27 ].…”