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Recent Research Papers of Note: Feb 1, 2007

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Journal: Microbiology, Feb 15
Title: Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis
Authors: SC Rison; J Mattow; PR Jungblut; NG Stoker
 
Authors demonstrate that protein translation start sites can be determined during protein identification by using MALDI-MS and MS/MS data to select the correct N-terminal sequence from a list of alternatives generated in silico.
 

 
Journal: Journal of Proteome Research, Jan. 27 [Epub ahead of print]
Title: Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy
Authors: PJ Boersema; N Divecha; AJ Heck; S Mohammed
 
Authors assess the potential of zwitterionic Hydrophilic Interaction LC as a first dimension for the analysis of complex peptide mixtures.
 

 
Journal: Analytical Chemistry, Jan. 24 [Epub ahead of print]
Title: Minimizing back exchange in (18)O(/16)O quantitative proteomics experiments by incorporation of immobilized trypsin into the initial digestion step
Authors: JR Sevinsky; KJ Brown; BJ Cargile; JL Bundy; JL Stephenson
 
Authors explore the use of immobilized trypsin in the initial digestion step as a means to minimizing post-labeling back exchange of 18-O-labeled peptides into the 16-O form when multidimensional peptide separation methods are incorporated into the sample workflow.
 

 
Journal: Molecular bioSystems, Feb. 3 [Epub Nov. 2, 2006]
Title: A cancer protein microarray platform using antibody fragments and its clinical applications
Authors: S Song; B Li; L Wang; H Wu; Hu; M Li; C Fan
 
Authors developed an antibody fragments microarray platform for serum tumor markers. The microarray platform is “quantitative, highly specific and reasonably sensitive. More importantly, clinical applications of our F(ab')(2) microarray platform for upwards of 100 patient serum samples clearly show its potential in cancer diagnostics,” according to the abstract.
 

 
Journal: Journal of Proteome Research, Jan. 23 [Epub ahead of print]
Title: Identifying pharmacodynamic protein markers of centrally active drugs in humans: A pilot study in a novel clinical model
Authors: ST Patil; RE Higgs; JE Brandt; MD Knierman; V Gelfanova; JP Butler; AM Downing; J Dorocke; RA Dean; WZ Potter; D Michelson; AX Pan; SS Jhee; JE Hale
 
Authors used mass spectrometry proteomics techniques capable of quantifying hundreds of proteins simultaneously in cerebrospinal fluid and plasma to evaluate the feasibility of measuring changes in proteins related to the administration of drugs.
 

 
Journal: Cancer Science, February 2007
Title: Biomarker discovery: A proteomic approach for brain cancer profiling
Authors: AA Khalil; P James
 
Authors used differential gel electrophoresis technology coupled with MALDI/TOF and LC/MS/MS to investigate tumor-specific changes in the proteome of human brain cancer. Authors say they found 20 proteins that were not known to be differentially expressed in human brain cancer. The proteins “provided novel information on the differences existing between normal brain and gliomas, and thus might prove to be useful molecular indicators of diagnostic or prognostic value,” according to the abstract.
 

 
Journal: Proteome Science, Jan. 16
Title: Methods for peptide identification by spectral comparison
Authors: J Liu; AW Bell; JJ Bergeron; CM Yanofsky; B Carrillo; CE Beaudrie; RE Kearney
 
Authors investigated computational issues related to comparing unknown experimental spectra to a library of previously identified spectra for the purposes of peptide sequencing in shotgun proteomics experiments.
 

 
Journal: Electrophoresis, Jan. 16 [Epub ahead of print]
Title: Shotgun electroelution: A proteomic tool for simultaneous sample elution from whole SDS-polyacrylamide gel slabs
Authors: J Antal; B Banyasz; Z Buzas
 
Authors describe a high-throughput device that allows parallel electroelution of separated SDAS-protein bands directly from intact unsectioned polyacrylamide gel slabs and single electroelution for some protein spots into a 384-well standard flat-bottom multiwell plate.
The device provides complete and quick elution for proteomics research from 1D and 2D gels without gel sectioning, the authors say. According to the abstract, the design is a “good candidate” for automation of spot elution “since there are no moving liquid containing components in the apparatus.”
 

 
Journal: Analytical Chemistry, Jan. 15
Title: MicroSPE-nanoLC-ESI-MS/MS using 10-microm-i.d. silica-based monolithic columns for proteomics
Authors: Q Luo; JS Page; K Tang; RD Smith
 
Authors developed silica-based monolithic capillary columns with integrated nanoESI emitters that provide high quality and robust microSPE-nanoLC-ESI-MS analyses. In an initial application with a linear ion trap MS, authors say they identified 5,500 unique peptides covering 1,443 distinct Shewanella oneidensis proteins from a 300 ng tryptic digest sample in a single 4-h LC-MS/MS analysis. 
 

 
Journal: Rapid Communications in Mass Spectrometry: RCM, Jan. 11 [Epub ahead of print]
Title: Direct identification of proteins from T47D cells and murine brain tissue by matrix-assisted laser desorption/ionization post-source decay/collision-induced dissociation
Authors: PH Pevsner; F Naftolin; DE Hillman; DC Miller; A Fadiel; A Kogus; A Stern; HH Samuels
 
Authors set out to determine the feasibility of direct MALDI identification of proteins in a fixed T47D breast cancer cells and murine brain tissues. Based on their results, they say that MALDI/PSD/CID, combined with bioinformatics, can be used for the direct identification of proteins from cells and tissues. “Refinement in preparation techniques may improve this approach to provide a tool for quantitative proteomics and clinical analysis,” they say in the abstract.
 

 
Journal: Genome Research, Jan. 25 [Epub ahead of print]
Title: Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry
Authors: VA Petyuk; WJ Qian; MH Chin; H Wang; EA Livesay; ME Monroe; JN Adkins; N Jaitly; DJ Anderson; DG Camp; DJ Smith; RD Smith
 
Authors describe a method for comprehensive spatial proteome mapping that addresses issues that have challenged prior imaging efforts such as throughput, sensitivity of applied analytical methodologies, and accurate quantitation of protein abundances across the brain. Authors use voxelation integrated with automated microscale sample processing, a high-throughput LC system coupled with a high-resolution FTICR MS, and a “universal” stable isotope labeled reference sample approach for robust quantitation.
 

 
Journal: Analytical Chemistry, Jan. 23 [Epub ahead of print]
Title: Bidimensional tandem mass spectrometry for selective identification of nitration sites in proteins
Authors: A Amoresano; G Chiappetta; P Pucci; M D’Ischia; G Marino
 
Authors describe a new approach for protein nitration involving dansyl chloride labeling of the nitration sites. The tryptic digest from the entire protein mixture is directly analyzed by MS on a linear ion trap MS while discrimination between nitro- and unmodified peptide is “based on two selectivity criteria obtained by combining a precursor ion scan and MS3 analysis.”