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Biological Sciences

Targeted (data-directed) LC-MS/MS

Sponsor: DOE Office of Biological and Environmental Research
Contact: Ljiljana Paša-Tolić

Proteome analyses of clinical samples are often limited by available sample sizes making targeted focus on identification of key features clearly attractive. Thus, a method is desired that focuses on identifying a limited subset of proteins that display significant changes in abundance ratios between two small tissue samples, analogous to selective MS analysis of spots from 2D gels that show significant changes between two gels.

We have recently developed hardware and corresponding software tools for targeted LC-FTICR proteome analysis to allow a set of initially unidentified peptides to be examined on the basis of their distinctive changes in abundance between two stable-isotopically labeled samples. Initially, two differentially labeled samples are analyzed by LC-FTICR-MS. Identified features that exhibit significant differences in MS intensities in the first analysis are characterized on the basis of both elution time and mass. This information is then used in a subsequent automated analysis where these "interesting" peptides are selected for MS/MS analysis. Thus, the identities of the flagged features can be determined without having to identify every feature by MS/MS. In turn, peptides identified on the basis of their distinctive peptide sequence uniquely identify their parent proteins and their potential biological relevance.

This process was recently exemplified by using a targeted MS/MS method to identify Shewanella oneidensis proteins that were differentially abundant as a result of growth under aerobic versus sub-oxic conditions (Masselon et al. 2005).


Masselon C, Paša-Tolić L, Tolić N, Anderson GA, Bogdanov B, Vilkov AN, Shen Y, Zhao R, Qian W-J, Lipton MS, Camp DGI, Smith RD. 2005. "Targeted comparative proteomics by liquid chromatography-Fourier transform ion cyclotron resonance tandem mass spectrometry." Analytical Chemistry 77:400-406.

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