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Recent Research Papers of Note: Jan 22, 2009

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Journal: Biotechnology and Applied Biochemistry, February
Title: Development of affinity columns for the removal of high-abundance proteins in cerebrospinal fluid
Authors: M Ramström; A Zuberovic; C Grönwall; J Hanrieder; J Bergquist; S Hober

Authors designed an affinity matrix for depleting high-abundance proteins found in cerebrospinal fluid. Five high-abundance CSF proteins were chosen: human serum albumin; IgG; transferrin; and transthyretin were combined in an affinity column. Polyclonal antibodies against cystatin C were also coupled to chromatographic beads and packed in a separate column. The authors reported highly reproducible and efficient removal of the five target proteins.


Journal: Analytical Chemistry, Jan. 15 [Epub ahead of print]
Title: Relationship between sample loading amount and peptide identification and its effects on quantitative proteomics
Authors: K Liu; J Zhang; J Wang; L Zhao; X Peng; W Jia; W Ying; Y Zhu; H Xie; F He; X Qian

Despite being crucial for the optimization of proteomics studies, the relationship between sample loading amount and peptide identification has been addressed in few studies. Here, the authors presented a systematic study using a replicate-run strategy "to probe the inherent influence of both peptide physicochemical properties and matrix effects on the relationship between peptide identification and sample loading amounts, as well as applications in protein quantification," according to the abstract.


Journal: Journal of Proteome Research, Jan. 13 [Epub ahead of print]
Title: Evaluation of the Variation in Sample Preparation for Comparative Proteomics Using Stable Isotope Labeling by Amino Acids in Cell Culture
Authors: G Zhang; D Fenyö; TA Neubert

Authors reported the strategy of stable isotope-labeling by amino acids in cell culture for evaluating the effect of the variation in sample preparation for quantitative proteomics. They first evaluated the reproducibility of immunoprecipitation and in-gel digestion, and characterized the impact of replicate number on quantitative accuracy. Then they evaluated the overall variation in a comparative workflow involving three sequential sample preparation steps — IP; SDS-PAGE fractionation; and in-gel digestion.


Journal: Proteomics, Jan. 13 [Epub ahead of print]
Title: Using the protein chip interface with quadrupole time-of-flight mass spectrometry to directly identify peaks in SELDI profiles — initial evaluation using low molecular weight serum peaks
Authors: J Peng; AJ Stanley; D Cairns; PJ Selby; RE Banks

Many studies using SELDI have been done to generate diagnostic serum profiles, according to the authors. While some results have shown promise, one limitation has been an inability to easily identify potential discriminatory peaks. For their study, the authors described "the first technical evaluation" of the ProteinChip interface coupled to an MS/MS platform which allows direct sequencing of peptides greater than 6,000 daltons, and the direct sequence identification of 21 peaks commonly seen in serum samples. They also described for the first time the use of on-chip acetylation to aid in validating sequence identification.


Journal: Journal of Proteome Research, Jan. 13 [Epub ahead of print]
Title: A Soft Preparative Method for Membrane Proteome Analysis Using Frit Inlet Asymmetrical Flow Field-Flow Fractionation: Application in a Prostatic Cancer Cell Line
Authors: D Kang; JS Yoo; MO Kim; MH Moon

Despite the important role that membrane proteins play in biological functions such as signal transduction and cell-cell interactions, a preparative method that produces a sufficient yield of purified membrane proteins remains a challenge, the authors said in the abstract. In their study, they used frit inlet asymmetrical fragments containing membrane proteins from free cytoplasmic proteins of prostatic cancer cell lysates. The isolated membrane proteins were digested and analyzed by nanoflow liquid chromatography-tandem mass spectrometry. They compared their method with a ultracentrifugation method and found that theirs resulted in more purified membrane proteins with fewer cytoplasmic proteins.


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Journal: Journal of Proteome Research, Jan. 9 [Epub ahead of print]
Title: Comparison of Three Commercially Available DIGE Analysis Software Packages: Minimal User Intervention in Gel-Based Proteomics
Authors: Y Kang; T Techanukul; A Mantalaris; JM Nagy

The study compared three commonly available DIGE-enabled software packages, DeCyder v6.5; Progenesis SameSpots v3.0; and Dymension3. According to the abstract, Progenesis SameSpots outperformed the other two software packages in matching accuracy. They also said that the results for protein fold changes were "substantially" different in each package "which indicates that in spite of using internal standards, quantification is software dependent." [See related story, this issue]


Journal: Proteomics, Jan. 9 [Epub ahead of print]
Title: Multivariate analysis of single quadrupole LC-MS spectra for routine characterization and quantification of intact proteins
Authors: FT Michaud; A Garnier; L Lemieux; C Duchesne

Proposed is a method based on the detection of intact, non-digested proteins by liquid chromatography coupled to single quadrupole MS, followed by the analysis of the resulting spectra by multivariate analysis. Using their method even large molecular-weight proteins that generate complex spectra can be characterized to a level that allows isoform discrimination, according to the abstract.


Journal: Proteomics, Jan. 9 [Epub ahead of print]
Title: A bioanalytical method for the proteome wide display and analysis of protein complexes from whole plant cell lysates
Authors: N Remmerie: L Roef; E Van De Slijke; J Van Leene; G Persiau; D Eeckhout; H Stals; K Laukens; F Lemière; E Esmans; H Van Onckelen; D Inzé; G De Jaeger; E Witters

Authors studied a method for the separation of protein complexes combining gel filtration and BN-PAGE. A non-denaturing extraction procedure was optimized for plant whole-cell matrices. "Hyphenation to denaturing electrophoresis and mass spectrometric analysis allows for the simultaneous identification of multiple (previously unidentified) protein interactions in single samples," the authors said in the abstract.


Journal: Molecular & Cellular Proteomics, Jan. 7 [Epub ahead of print]
Title: A human proteome detection and quantitation project: hPDQ
Authors: NL Anderson; NG Anderson; TW Pearson; CH Borchers; AG Paulovich; SD Patterson; M Gillette; R Aebersold; SA Carr

According to the abstract, the lack of sensitive, specific, multiplexable assays for most human proteins is "the major barrier impeding development of candidate biomarkers into clinically useful tests." A complete suite of assays, for example, two peptides from each protein product for each of the approximately 20,500 human genes, would allow for rapid and systematic verification of candidate biomarkers, the authors said. It also would lay a quantitative foundation for subsequent efforts to define splice variants, post-translational modifications, protein-protein interactions, and tissue localization. [See related story, this issue]


Journal: Journal of Proteome Research, Jan. 2
Title: Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an (18)O-Labeled "Universal" Reference Sample
Authors: WJ Qian; T Liu; VA Petyuk; MA Gritsenko; BO Petritis; AD Polpitiya; A Kaushal; W Xiao; CC Finnerty; MG Jeschke; N Jaitly; ME Monroe; RJ Moore; LL Moldawer; RW Davis; RG Tompkins; DN Herndon; DG Camp; RD Smith

"The quantitative comparison of protein abundances across a large number of biological or patient samples represents an important proteomics challenge that needs to be addressed for proteomics discovery applications," according to the abstract. Described is a method incorporating stable isotope (18) O-labeled "universal" reference sample as a comprehensive set of internal standards for the analysis of large sample sets quantitatively.