Journal: Metabolites

Article Title: An Open-Source Pipeline for Processing Direct Infusion Mass Spectrometry Data of the Human Plasma Metabolome

doi: 10.3390/metabo12080768

Figure Lengend Snippet: The order of launching programs for processing DIMS (ESI-QTOF, maXis Impact II, Bruker Daltonics) mass spectra. On the left (purple), a pipeline with the commercial COMPASS DataAnalysis program, and the MatLab development environment is shown. On the right (green)—the MALDIquant package together with MetaboAnalystR/Mummichog R language module. The numbers in the squares indicate the data processing steps described in the text.

Article Snippet: The studied spectra were acquired using ESI-QTOF maXis Impact II (Bruker Daltonics, Billerica, MA, USA), then pre-processed using COMPASS/DataAnalysis commercial software and mapped onto the metabolites using in-lab-developed MatLab scripts.

Techniques:

Journal: Metabolites

Article Title: An Open-Source Pipeline for Processing Direct Infusion Mass Spectrometry Data of the Human Plasma Metabolome

doi: 10.3390/metabo12080768

Figure Lengend Snippet: The number of peaks detected using different intensity smoothing and noise estimation algorithms.

Article Snippet: The studied spectra were acquired using ESI-QTOF maXis Impact II (Bruker Daltonics, Billerica, MA, USA), then pre-processed using COMPASS/DataAnalysis commercial software and mapped onto the metabolites using in-lab-developed MatLab scripts.

Techniques:

Journal: Metabolites

Article Title: An Open-Source Pipeline for Processing Direct Infusion Mass Spectrometry Data of the Human Plasma Metabolome

doi: 10.3390/metabo12080768

Figure Lengend Snippet: Enriched metabolic pathways in the third stage of obesity, MetaboAnalyst 4.0/5.0, web-version. ( a ) DIMS mass-spectra after processing with the DataAnalysis/MatLab pipeline were analyzed by the MSEA tool. ( b ) DIMS mass-spectra after MALDIquant/Mummichog pipeline processing were analyzed with the Pathway Analysis tool. “Match Status” indicates the number of annotated metabolites/number of known metabolites of the KEGG pathway.

Article Snippet: The studied spectra were acquired using ESI-QTOF maXis Impact II (Bruker Daltonics, Billerica, MA, USA), then pre-processed using COMPASS/DataAnalysis commercial software and mapped onto the metabolites using in-lab-developed MatLab scripts.

Techniques:

Journal: Molecular & Cellular Proteomics : MCP

Article Title: A Human Lectin Microarray for Sperm Surface Glycosylation Analysis *

doi: 10.1074/mcp.M116.059311

Figure Lengend Snippet: The identification of Galectin-1 recognized membrane-associated proteins by LC-MS/MS analysis. A, LC-MS/MS was used to identify the galactosylations of the membrane-associated proteins captured by galectin-1. B, LC-MS/MS spectrum of two peptides. The corresponding proteins were identified as HSP90A and HSP90B. C, Anti-HSP90 antibody specific recognized HSP90 from sperm cell lysate. D, Localization of HSP90 with galectin-1 and anti-HSP90 antibody. Sperms were incubated with biotinylated galectin-1 and anti-HSP90 antibody simultaneously, the results of galcetin-1 and HSP90 were then visualized by Cy3-streptavidin and a Cy5 conjugated second antibody specific for the anti-HSP90, respectively.

Article Snippet: The mass spectrometer was set as one full MS scan followed by ten MS/MS scans on the ten most intense ions from the MS spectrum with the following dynamic exclusion settings: repeat count = 2, repeat duration = 15 s, exclusion duration = 30 s. The raw data were extracted using LC/MS software DataAnalysis 4.1 (Bruker Compass software) and converted into mgf files for further MASCOT 2.4 (Matrix Science, Boston, MA) search.

Techniques: Liquid Chromatography with Mass Spectroscopy, Incubation