Project description:The PRM dataset corresponds to the raw data files supporting the comparison between conventional database search using Mascot and spectral matching strategy (Figure 3). The PRM and DDA raw data files support the comparison between these two acquisition methods using the spectral matching strategy to corroborate the identity of the peptides (Figure 4D). The data were generated from the triplicate analyses of a dilution series of 778 SIL peptides spiked in a yeast tryptic digest at concentrations ranging from 50 amol/µL to 37 fmol/µL.
Project description:Analysis of small RNAs with 5'p, 3'OH Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE20341
Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. To benchmark this method, we measured twenty pure culture species using the Direct Protein-SIF method as well as Isotope Ratio Mass Spectrometry. Some of the pure cultures were measured in technical replicates to see how consistent Protein-SIF measurements are between mass spec runs. This submission thus contains 29 raw files for the pure cultures. See table in the submission for details of which species was measured for which .raw file. We also included the Direct Protein-SIF specific isotope pattern files as well as the .mzML files and PSM files required as input for the Direct Protein-SIF software. In addition to the pure culture a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are also included in this submission (see publication for details on how the reference material is used to calibrate the method).
Project description:Targeted metabolomics platforms included amino acids and metabolites related to glucose-mediated energy production. The targeted metabolome changed with chemotheraphy-induced cachexia, and the changes were reversed with potential treatment of the cachexia. .rdb files were included as raw data files where detailed information regarding MRM transitions and internal standards can be found. Several amino acids (Gly, Pro, Gln, Taurine) were analyzed after dilution because their peak intensities were too high. Thus their analysis was performed separately from other amino acids, and their rdb files were saved in separate rdb files.
Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports
Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.
2017-01-27 | E-PROT-2 | biostudies-arrayexpress
Project description:Mock microbial community dilution series
Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.