PRIDE Assigned Tags:Biomedical Dataset
Visualize in PRIDE Inspector
1.Download, uncompress and open PRIDE Inspector
2.Click in the magnifier on the left top corner, paste the project or assay that you would like to open in the search box, and hit search
3.Click in the corresponding "Download" button to download the files and visualize them
Discovery of new cerebrospinal fluid biomarkers for meningitis in children C4PR_LIV
Bacterial meningitis is usually fatal without treatment and prompt and accurate diagnosis coupled with the timely administration of parenteral antibiotics, are necessary in order to save lives. The diagnosis can sometimes be delayed whilst samples are analysed in a laboratory using traditional methods of microscopy and antigen testing. The objective of our project is to define specific protein signatures in cerebrospinal fluid associated with Streptococcus pneumoniae infection which could lead to the development of assays or point-of-care devices to improve the speed and accuracy of diagnosis, and guide the clinicians in the treatment and prognosis of children with bacterial meningitis. The associated research paper is in preparation.
Sample Processing Protocol
CSF samples were centrifuge within 2 h of collection and the supernatant fraction was frozen within 4 h of collection, and stored at -80 °C until analysis. Samples (20 L in 200 L total volume) were subjected to in-solution digestion and 0.5 L was analyzed using the ‘Top20’ protocol on DDA mode in an LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific).
Data Processing Protocol
The raw data acquired were converted into a single *.mgf format file containing the peaklist by Proteome Discoverer 1.1 (Thermo Fisher Scientific) using default parameters. Independent *.mgf files for each sample were searched against a merged database composed of reviewed entries of Human Uniprot database (version 20120711; 20,225 entries) and Streptococcus pneumoniae reference strain ATCC BAA-255/R6 (version 20120711; 2,029 entries) with MASCOT search engine (version 2.4.0, Matrix Science), using trypsin as the enzyme, carbamidomethylation of cysteine as fixed modification, allowing methionine oxidation as variable modification and one trypsin missed cleavage, a mass tolerance of 10 ppm for precursors and 0.6 Da for fragment ions. The false discovery rate (FDR) was calculated using the decoy database tool in MASCOT. The outputs from MASCOT were saved in mzIdentML format. The peptides and proteins were quantified using Progenesis LCMS software (version 4.0; Nonlinear Dynamics). Software default thresholds were used. Samples were grouped as control (n=4) and infected (n=8). Features with positive charge states between +2 and +5, and three or more isotopic peaks were taken to further identification. A merged peak list generated by Progenesis LCMS was searched against the composite database, using MASCOT search engine (version 2.4.0, Matrix Science). Trypsin was selected as the enzyme, carbamidomethylation of cysteine as fixed modification, allowing methionine oxidation as variable modification and one trypsin missed cleavage, mass tolerance of 10 ppm for precursors and 0.6 Da for fragment ions. MASCOT results were imported into Progenesis LCMS and a cut off score of 20 was applied after manually evaluating the quality of the lowest score peptides. Similar proteins were grouped and only non-conflicting features were used for quantification. The output Progenesis peptide and protein CSV files were imported to Progenesis Post-Processor version 1.0.4-beta (http://progenesis-post-processor.googlecode.com/svn/maven/release/progenesis-post-processor/1.0.4-beta/progenesis-post-processor-1.0.4-beta.zip) for conversion to mzQuantML file.
Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA. Standardization and Guidelines: How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics. 2014 Jul 21 PubMed: 25047258
|#||Accession||Title||Proteins||Peptides||Unique Peptides||Spectra||Identified Spectra||View in Reactome|
|1||34937||no assay title provided (mzIdentML)||307||9495||2551||15738||7488||
|2||34938||no assay title provided (mzIdentML)||30||432||199||13327||430||
|3||34939||no assay title provided (mzIdentML)||257||7789||1758||12872||6445||
|4||34946||no assay title provided (mzIdentML)||188||5058||1151||10426||4348||
|5||34947||no assay title provided (mzIdentML)||406||11003||3768||19566||8245||
|6||34944||no assay title provided (mzIdentML)||379||11701||4185||21771||9091||
|7||34945||no assay title provided (mzIdentML)||547||12291||4845||17057||8785||
|8||34936||no assay title provided (mzIdentML)||472||11395||4370||18729||8586||
|9||34942||no assay title provided (mzIdentML)||250||9736||2309||17806||7075||
|10||34943||no assay title provided (mzIdentML)||419||10909||3569||19491||8530||