Proteomics

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TurboRAW2MGF: Removing isobaric-related ions improves the peptide/protein identification

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Rattus Norvegicus (rat) Homo Sapiens (human)

TISSUE(S): Liver

SUBMITTER: Quanhu Sheng  

LAB HEAD: Quanhu Sheng

PROVIDER: PXD000994 | Pride | 2015-01-30

REPOSITORIES: Pride

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Dataset's files

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20110915_iTRAQ_4plex_GK_6ug_Exp_1.dat-pride.pride.mgf.gz Mgf
20110915_iTRAQ_4plex_GK_6ug_Exp_1.dat-pride.pride.mztab.gz Mztab
20110915_iTRAQ_4plex_GK_6ug_Exp_1.dat-pride.xml.gz Xml
20110915_iTRAQ_4plex_GK_6ug_Exp_1.raw Raw
20110915_iTRAQ_4plex_GK_6ug_Exp_2.dat-pride.pride.mgf.gz Mgf
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Publications

Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data.

Sheng Quanhu Q   Li Rongxia R   Dai Jie J   Li Qingrun Q   Su Zhiduan Z   Guo Yan Y   Li Chen C   Shyr Yu Y   Zeng Rong R  

Molecular & cellular proteomics : MCP 20141130 2

Isobaric labeling techniques coupled with high-resolution mass spectrometry have been widely employed in proteomic workflows requiring relative quantification. For each high-resolution tandem mass spectrum (MS/MS), isobaric labeling techniques can be used not only to quantify the peptide from different samples by reporter ions, but also to identify the peptide it is derived from. Because the ions related to isobaric labeling may act as noise in database searching, the MS/MS spectrum should be pr  ...[more]

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