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
TurboRAW2MGF: Removing isobaric-related ions improves the peptide/protein identification
Isobaric labelling technique coupled with high resolution mass spectrometry has been widely employed in the proteomics workflows requiring relative quantification. For each high resolution tandem mass spectrum (MS/MS), it can be used not only to quantify the peptide from different samples by reporter ions，but also to identify the peptide it derived from. Since isobaric related ions act as noises in database searching, the MS/MS spectrum should be preprocessed before peptide/protein identification. In this paper, we demonstrated that there were a lot of high frequency, high abundance isobaric related ions in MS/MS spectrum. By combining removing isobaric related ions with deisotoping and deconvolution in MS/MS preprocessing procedure, the peptide/protein identification sensitivity improved significantly. A user-friendly software TurboRaw2MGF (v2.0) has been implemented for converting raw TIC data files to mascot generic format files which can be downloaded for free from https://github.com/shengqh/RCPA.Tools/releases as part of the software suite ProteomicsTools.
Sample Processing Protocol
Proteins were extracted from GK rat liver tissue and digested by trypsin. The peptide mixture was labelled by iTRAQ-plex4 or iTRAQ-plex8. An LTQ-Orbitrap Velos was used for LC-MS/MS analysis.
Data Processing Protocol
TurboRAW2MGF was used for extracting tandem mass spectra from raw files. Using Mascot algorithm, all MS/MS spectra were searched against a composite target-decoy rat Uniprot database. BuildSummary was used to generate a confident protein list for both peptide and protein with a false discovery rate ≤ 0.01.
iodoacetamide derivatized residue
iTRAQ4plex-116 reporter+balance reagent acylated residue
iTRAQ8plex-116 reporter+balance reagent acylated residue
TMT6plex-126 reporter+balance reagent acylated residue
Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R. Preprocessing significantly improves the peptide/protein identification sensitivity of high resolution isobarically labeled tandem mass spectrometry data. Mol Cell Proteomics. 2014 Nov 30. pii: mcp.O114.041376 PubMed: 25435543
|#||Accession||Title||Proteins||Peptides||Unique Peptides||Spectra||Identified Spectra||View in Reactome|
|1||36883||iTRAQ4 replicate 1||4778||16683||9303||22572||9673||
|2||36884||iTRAQ4 replicate 2||4663||15703||8687||21449||8838||
|3||36885||iTRAQ4 replicate 3||4656||15558||8832||21244||8902||
|4||36886||iTRAQ8 replicate 1||1614||7174||4101||18956||5292||
|5||36880||iTRAQ8 replicate 2||1537||7266||4109||19479||5429||
|6||36882||iTRAQ8 replicate 3||1507||6542||3814||18342||4894||
|7||36881||TMT6 for HCC||3341||13916||6431||35184||11732||