ABSTRACT: Data was acquired using Q Exactive and C18 RP-UHPLC in positive mode.
mzXML files only.
Data used a test set for Ion Identity Molecular Networking.
Project description:Non-targted metabolomics from extracts from B. subtilis wildtype and SRF knock-out mutant. Data processed with MZMine2 and Ion Identity Networking.
Project description:Interventions: Population:Nil
Primary outcome(s): Molecular binding profile on NuTECs of molecules present in patient urine.
Study Design: Diagnostic test for accuracy
Project description:This SuperSeries is composed of the following subset Series:; GSE11440: Role of Caveolin 1, E-Cadherin, Enolase 2 and PKCa on resistance to methotrexate in human HT29 colon cancer cells; GSE16066: Networking of differentially expressed genes in CaCo2 human colon cancer cells resistant to methotrexate; GSE16070: Networking of differentially expressed genes in human MCF7 breast cancer cells resistant to methotrexate; GSE16080: Networking of differentially expressed genes in human MDA-MB-468 breast cancer cells resistant to methotrexate; GSE16082: Networking of differentially expressed genes in human MIA PaCa2 pancreatic cancer cells resistant to methotrexate; GSE16085: Networking of differentially expressed genes in human K562 erythtoblastic leukemia cells resistant to methotrexate; GSE16089: Networking of differentially expressed genes in human Saos-2 osteosarcoma cells resistant to methotrexate Experiment Overall Design: Refer to individual Series
Project description:Intact proteins, as well as Glu-C, and Lys-C/trypsin-derived peptides extracted from developing soybean seeds were immunoenriched using antibodies against acetyllysine residues. Enriched proteins were separated by SDS-PAGE prior to tryptic digestions and enriched peptides were analyzed directly, in both cases using a Thermo LTQ-Orbitrap XL. In separate LC-MS/MS runs fragmentation was achieved using CID, ETD, or a combination of the two mediated by a data-dependent decision tree. Individual RAW files were converted to mzXML format for mining with MS-GFDB (v2012.06.07) using default settings of the msconvert executable within the Trans-Proteomic Pipeline v4.6. Searches with MS-GFDB were performed with default methods and parameters, except as noted: number of allowed isotope errors was set at zero, and fully enzymatic peptides were specified, i.e. no non-enzymatic termini. Data mining was additionally performed with a local Mascot server, v2.3.1, and ZCore v1.17, both accessed through Proteome Discoverer v1.3 (Thermo Scientific), as well as Sequest HT v1.3, a reimplementation of SEQUEST within Proteome Discoverer v1.4. Tandem mass spectra were searched in Proteome Discoverer with allowed missed cleavages set to four. Prior to Mascot and Sequest searches, ETD spectra were further filtered to remove peaks resulting from precursors, charge-reduced precursors, and neutral losses thereof with mass windows of 4 Da, 2 Da, and 2 Da, respectively.