Project description:We analyzed total proteome of three methyltransferase gene knockouts strains of Escherichia coli: ΔrsmF (JW5301), ΔrlmC (JW2756), ΔrlmE (JW3146) from Keio collection and wild type (WT). Proteins were assessed using IDA approach (i.e. Information Dependent Acquisition) and SWATH (Data-Independent Acquisition) on Sciex TripleTof 5600+ mass‐spectrometer with a NanoSpray III ion source (ABSciex, Canada) coupled to a NanoLC Ultra 2D+ nano‐HPLC system (Eksigent). Dataset covers 16 samples.
Project description:Three iTRAQ8plex experiment replicate using TripleToF 5600 system. Protein identification were performed using the ProteinPilot software (version 4.0.8085,Paragon Algorithm version 4.0.0.0).All MS/MS spectra was search against amino acids sequences which is annotated from genome. The search parameters was set as follows: Cys. Alkylation: Iodoacetic acid, Digestion: Trypsin, ID Focus: Biological modifications, Search Effort: Thorough. The search results was filter using Local FDR 5%.
Project description:To compare mouse saliva and induced salivary gland from PSCs (iSG) secreted protein profiles, those samples were digested by Lys-C and trypsin and then analyzed by data-dependent acquisition (DDA) and sequential window acquisition of all theoretical mass spectra (SWATH) using TripleTOF 5600+ mass spectrometer coupled with nanoLC.
Project description:This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics", Nature Methods, in press Raw files are deposited here in ProteomeXchange and are associated with the DIA-Umpire processed data. All DIA-Umpire processed results for each sample together with DDA results are deposited in separated folders. Also see the "DataSampleID.xlsx" associated with this Readme file. Internal reference from the Gingras lab ProHits implementation: Project 94, Export version VS2 (Tsou_DIA-Umpire)
Project description:This study investigates the proteomic alterations in striatal synaptic mitochondria isolated from 3-month-old wild-type and Pink1 KO rats using the SWATH-MS strategy. This dataset consists of 32 raw MS files, comprising 8 DIA (SWATH) and 24 DDA runs on a TripleTOF 5600 (SCIEX). Our findings revealed synaptic mitochondrial proteomic changes due to loss of Pink1.
Project description:Genus-wide proteomics analysis of cobra (Naja) venoms. For top-down analysis, venom samples were reduced with TCEP and measured via HPLC-MS/MS (Q-Exactive) . Spectrum-Protein matching was performed with TopPic1.1 against a genus wide translated transcriptome database and NCBI protein entries from the najas.
For bottom-up analysis, HPLC separated fraction of venom were dried down, reduced with triethylphosphine and alkylated with 2-iodoethanol. HPLC-MS/MS experiments were performed on normalflow UHPLC-QTOF system (AB Sciex 5600 TripleTOF). Data analysis (PSM) was performed ProteinPilot version 4.0 and the transcriptome derived protein sequence database.
Project description:Untargeted metabolomics profiling of mice urine after 5 Gy and 7.5 Gy total body radiation exposure at 24 hours. Metabolic profiling of urine samples were performed by TripleTOF 5600+ (AB Sciex) in both ionization mode
Project description:Nitrogen cavitation of bovine sperm to isolate plasma membrane. FASP digestion using trypsin. Data acquired using 5 workflows: (1) Unfractionated on a 5600 TripleTOF; (2) SCX-ESI-LC-MS/MS on a QSTAR Elite; (3) 1D Gel-LC-ESI-LC-MS/MS on a QSTAR Elite; (4) SCX-LC-MALDI-MS/MS on a UltrafleXtreme; (5) 1D Gel-LC-MALDI-MS/MS on a UltrafleXtreme
Project description:HyD-LIR-Venus consists of HyD, a short hydrophobic domain of Aplysia phosphodiesterase 4 short-form; LIR of TP53INP2; and a fluorescent protein, Venus. This protein efficiently binds to LC3-II and GABARAP-II localizing on inner membrane of autophagosomes and does not affect autophagosome formation.Liver samples prepared from liver-specific HyD-LIR expressing mice together with the control mice were analyzed by mass spectrometry (TripleTOF 5600) coupled to Ekspert nanoLC 415 system with Ekspert cHipLC (Sciex, Framingham, MA). The analysis results were searched against the UniProt database (release 2019_11) using ProteinPilot 5.0.2. software (Sciex). The library contained 2619 protein groups with the cutoff of 1% false discovery rate.