Project PXD000994

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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 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.


Quanhu Sheng, Vanderbilt University
Quanhu Sheng, Shanghai Institutes for Biological Sciences ( lab head )

Submission Date


Publication Date



    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


Showing 1 - 7 of 7 results
# 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