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Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data.

ABSTRACT: We investigated and compared three approaches for shotgun protein identification by combining MS and MS/MS information using LTQ-Orbitrap high mass accuracy data. In the first approach, we employed a unique mass identifier method where MS peaks matched to peptides predicted from proteins identified from an MS/MS database search are first subtracted before using the MS peaks as unique mass identifiers for protein identification. In the second method, we used an accurate mass and time tag method by building a potential mass and retention time database from previous MudPIT analyses. For the third method, we used a peptide mass fingerprinting-like approach in combination with a randomized database for protein identification. We show that we can improve protein identification sensitivity for low-abundance proteins by combining MS and MS/MS information. Furthermore, "one-hit wonders" from MS/MS database searching can be further substantiated by MS information and the approach improves the identification of low-abundance proteins. The advantages and disadvantages for the three approaches are then discussed.

SUBMITTER: Lu B

PROVIDER: S-EPMC3509208 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature

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Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data.

Lu Bingwen B Motoyama Akira A Ruse Cristian C Venable John J Yates John R JR

Analytical chemistry 20080215 6

We investigated and compared three approaches for shotgun protein identification by combining MS and MS/MS information using LTQ-Orbitrap high mass accuracy data. In the first approach, we employed a unique mass identifier method where MS peaks matched to peptides predicted from proteins identified from an MS/MS database search are first subtracted before using the MS peaks as unique mass identifiers for protein identification. In the second method, we used an accurate mass and time tag method b ...[more]

PMID: 18275164

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Project description:Pruni Semen, the seed of several unique Prunus plants, is a traditional purgative herbal material. To determine the authentic sources of Pruni Semen, 46 samples from four species were collected and analyzed. Ten compounds including multiflorin A (Mul A), a notable purative compound, were isolated and identified by chemical separation and nuclear magnetic resonance spectroscopy. Seventy-six communal components were identified by ultra-high performance liquid chromatography with linear ion trap-quadrupole Orbitrap mass spectrometry, and acetyl flavonoid glycosides were recognized as characteristic constituents. The flavonoids were distributed in the seed coat and cyanogenic glycosides in the kernel. Based on this, methods for identifying Pruni Semen from different sources were established using chemical fingerprinting, quantitative analysis of the eight principal compounds, hierarchical cluster analysis, principal component analysis, and orthogonal partial least squares discriminant analysis. The results showed that the samples were divided into two categories: one is the small seeds from Prunus humilis (Ph) and Prunus japonica (Pj), and the other is the big seeds from Prunus pedunculata (Pp) and Prunus triloba (Pt). The average content of Mul A was 3.02, 6.93, 0.40, and 0.29 mg/g, while the average content of amygdalin was 18.5, 17.7, 31.5, and 30.9 mg/g in Ph, Pj, Pp, and Pt, respectively. All the above information suggests that small seeds might be superior sources of Pruni Semen. This is the ﬁrst comprehensive report on the identiﬁcation of chemical components in Pruni Semen from different species. Graphical abstract Image 1 Highlights • Chemical constituents of Pruni semen from four Prunus species were compared.• Acetyl flavonoid glycosides were identified as the characteristic components.• Flavonoids were present in the seed coat and cyanogenic glycosides in the kernel.• The content of acetyl flavonoid in small seeds is significant higher than those in big ones.

Dataset Information

Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data.

Publications

Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data.

Similar Datasets

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