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Recent Research Papers of Note: Mar 19, 2010

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Journal: Analytical Chemistry, March 10 [Epub ahead of print]
Title: N,N-dimethyl leucines as novel isobaric tandem mass tags for quantitative proteomics and peptidomics
Authors: F Xiang; H Ye; R Chen; Q Fu; L Li

Describes the development and application of a set of "novel N, N-dimethyl leucine 4-plex isobaric tandem mass tagging agents with high quantitation efficacy and greatly reduced cost for neuropeptide and protein analysis," according to the abstract. The reagents are meant to be used as alternatives to iTRAQ and TMT technology "due to their synthetic simplicity, labeling efficiency, and improved fragmentation efficiency."


Journal: BMC Medical Genomics, March 10 [Epub ahead of print]
Title: mspecLine: bridging knowledge of human disease with the proteome
Authors: J Handcock; EW Deutsch; J Boyle

Describes mspecLine, "a tool that combines knowledge about human disease in Medline with empirical data about the detectable human proteome in PeptideAtlas," the authors said in the abstract. By calculating the semantic distance between annotated terms from a controlled biomedical laboratory, mspecLine is able to associate diseases with proteins. "We used an established semantic distance measure that is based on the co-occurrence of disease and protein terms in the Medline bibliographic database," the authors said.


Journal: Journal of Proteome Research, March 10, [Epub ahead of print]
Title: Comparison of a protein-level and peptide-level labeling strategy for quantitative proteomics of synaptosomes using isobaric tags
Authors: O Engmann; J Campbell; M Ward; PK Giese; AJ Thompson

Authors compare a protein-level-labeling GeLC-MS/MS strategy with a peptide-labeling 2DLC-MS/MS approach, using mouse hippocampus synaptosomes and isobaric tandem mass tags. Protein-level labeling resulted in 697 proteins, compared to 241 with peptide-level labeling. Importantly for quantitation, the authors said, protein-level labeling identified twice as many proteins, 480, as peptide-level labeling, which identified 232 peptides.


Journal: Electrophoresis, March 9 [Epub ahead of print]
Title: Delta2D and Proteomweaver: Performance evaluation of two different approaches for 2-DE analysis
Authors: R Millioni; M Miuzzo; S Sbrignadello; E Murphy; L Puricelli; A Tura; E Bertacco; M Rattazzi; E Iori; P Tessari

Authors compared two software packages, Delta2D from Decondon and Proteomweaver from Definiens, using both standard and experimental gel images. "Using standard gel images, the false negative spot count was 50 percent lower, the false positive count was 77 percent lower, the true positive count was 19 percent higher and spot matching was 4 percent higher in Delta2D when compared to Proteomeweaver," they said in the abstract. Using experimental gel images, they found that the time needed for a complete analysis with Delta2D was 30 percent that of the time needed with Proteomweaver. Few user interventions were required, as well.


Journal: Proteomics, March 9 [Epub ahead of print]
Title: Stopping the clock on proteomic degradation by heat treatment at the point of tissue excision
Authors: RJ Goodwin; AM Lang; H Allingham; M Borén; AR Pitt

Authors evaluated the "effectiveness of rapid and controlled heating of intact tissue to inactivate native enzymatic activity and prevent proteome degradation," according to the abstract. Using mouse brains and MALDI-MS, they found that protein and peptide markers were "seen to be stabilized" when the tissue was heat-treated prior to snap-freezing. "Thus, heat-treatment of tissue at time of excision is shown to prevent subsequent uncontrolled degradation of tissue at the proteomic level prior to any quantitative analysis, and to be compatible with downstream proteomic analysis," the authors said.


Journal: BMC Bioinoformatics, March 5 [Epub ahead of print]
Title: A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry
Authors: C Pan; BH Park; WH McDonald; PA Carey; JF Banfield; NC Verberkmoes; RL Hettich; NF Samatova

Describes a de novo sequencing algorithm, Vonode, developed specifically for analyzing high-resolution MS/MS spectra. The authors propose a scoring system to evaluate sequence tags based on mass accuracy information of fragment ions, in order to "fully exploit" the high mass accuracy of these spectra. The Vonode algorithm is available here.


Journal: Cell, March 5
Title: Protein dynamics in drug combinations: a linear superposition of individual-drug responses
Authors: N Geva-Zatorsky; E Dekel; AA Cohen; T Danon; L Cohen; U Alon

While drug and drug combinations have "complex biological effects on cells and organisms," little is known about how drugs affect protein dynamics that determine these biological effects, the authors said in the abstract. Using a dynamic proteomics approach, they investigate the response of human cells to 13 different drugs on 15 protein levels. The authors found that protein dynamics in response to drug combinations are "described accurately by a linear superposition of their response to individual drugs." They show that the dynamics in a three- or four-drug combination can be predicted based on the dynamics in drug pairs. "Our approach might eliminate the need to increase the number of experiments exponentially with the number of drugs and suggests that it might be possible to rationally control protein dynamics with specific drug combinations," the authors said.

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Journal: Journal of Proteome Research, March 5
Title: Value of using multiple proteases for large-scale mass spectrometry-based proteomics
Authors: DL Swaney; CD Wenger; JJ Coon

As a way of improving both protein identification and characterization in S. cerevisiae, the authors examined the use of multiple proteases instead of a single protease. The proteases used were trypsin, LysC, ArgC, AspN, and GluC. They used a data-dependent, decision tree-based algorithm "to tailor the MS2 fragmentation method to the peptide precursor," and identified 92,095 unique peptides mapping to 3,908 proteins at a false discovery rate of 1 percent. The results were a "significant improvement" over data from a single protease digest, which identified 27,822 peptides mapping to 3,313 proteins. "We demonstrate that large portions of the proteome are simply inaccessible following digestion with a single protease and that multiple proteases, rather than technical replicates, provide a direct route to increase both protein identifications and proteome sequence coverage," the authors said.


Journal: Journal of Proteome Research, March 5
Title: Secretomic and proteomic analysis of potential breast cancer markers by two-dimensional differential gel electrophoresis
Authors: TC Lai; HC Chou; YW Chen; TR Lee; HT Chan; HH Shen; WT Lee; ST Lin; YC Lu; CL Wu; HL Chan

The authors used 2D-DIGE and MALDI-TOF MS techniques to quantify and identify differentially expressed extracellular secreted proteins and total cellular proteins across non-invasive breast cancer cells, invasive breast cancer cells, and normal breast cells. In addition to identifying 50 unique differentially expressed proteins from three different media, they identified 133 unique differentially expressed proteins from total cellular proteins.


Journal: Journal of Proteome Research, March 5
Title: Prioritization of candidate protein biomarkers from an in vitro model system of breast tumor progression toward clinical verification
Authors: TY Lau; KA Power; S Dijon; I de Gardelle; S McDonnell; MJ Duffy; SR Pennington; WM Gallagher

Using in vitro cell culture model systems has resulted in numerous candidate biomarkers for various disease phenotypes, according to the abstract. However, assessing these biomarkers in patient samples, such as tissue or blood, may be impossible because the number of such candidate biomarkers is too large. Presented is a proteomic approach for discovering and prioritizing candidate markers that are more likely to be found in serum. They use a combination of experimental and in silico approaches to demonstrate this approach using an isogenic cell culture model of breast cancer invasion.


Journal: Analytical and Bioanalytical Chemistry, March 4 [Epub ahead of print]
Title: Novel molecular tumor classification using MALDI-mass spectrometry imaging of tissue microarray
Authors: MC Djidja; E Claude; MF Snel; S Francese; P Scriven; V Carolan; MR Clench

MALDI-IMS-MS profiling and imaging methodology was used to "visualize the distribution of several peptides and identify them directly from [tissue microarray] sections after on-tissue tryptic digestion," according to the abstract. A novel approach, which combines MALDI-IMS-MS and principal component analysis-discriminant analysis is described, "which has the aim of generating tumor classification models based on protein profile patterns."


Journal: Journal of Proteome Research, March 4 [Epub ahead of print]
Title: Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics
Authors: A Bertsch; S Jung; A Zerck; N Pfeifer; S Nahnsen; C Henneges; A Nordheim; O Kohlbacher

While multiple-reaction monitoring allows researchers to overcome problems associated with shotgun proteomics, developing MRM quantitation assays is time-consuming "because relevant peptide representatives of the proteins must be found and their retention time and the product ions must be determined," the authors said in the abstract. "Given the transitions, hundreds to thousands of them can be scheduled into one experiment run," they added, and selecting which transitions in an experiment should be included in a measurement can be difficult. The authors present a novel algorithm that allows the construction of MRM assays from the sequence of the targeted proteins alone, enabling the rapid development of targeted MRM experiments "without large libraries of transitions or peptide spectra."


Journal: Journal of Proteomics Research, March 2 [Epub ahead of print]
Title: Development of a new magnetic beads-based immunoprecipitation strategy for proteomics analysis
Authors: A Molares Vila; P Rupérez Pérez de Arrilucea; E Caso Peláez; A Gago Martínez

"Sample pre-treatment is a critical step for an efficient and reliable analysis and it is highly dependent on the complexity of the matrix," the authors said in the abstract. They present an immunoprecipitation approach using a new magnetic beads-based format, "which allows a selective/specific extraction of potential biomarkers from metastatic prostate cancer."


Journal: Proteomics, March 2 [Epub ahead of print]
Title: Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of mass spectrometry data
Authors: M Askenazi; S Li; S Singh; JA Marto

Improvements in proteomics technologies have yielded datasets that "far exceed the capabilities of typical low-throughput interpretation strategies," according to the abstract. Tools designed to leverage the peptide-centric content of mass spec-based proteomics trail behind the current rate of data production, however. The authors described Pathway Palette, "a freely accessible internet application that enables researchers to easily transition from peptides to biological pathways, while simultaneously retaining the qualitative and quantitative aspects of the underlying mass spectrometry data," they said.

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