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Recent Research Papers of Note in Proteomics: May 31, 2007

Journal: Journal of Psychiatric Research, September 2007, [Epub June 5, 2006]
Title: Comparative proteomic analysis with postmortem prefrontal cortex tissues of suicide victims
Authors: K Schlicht; A Buttner; F Siedler; B Scheffer; P Zill; W Eisenmenger; M Ackenheil; B Bondy
Using 2D gel electrophoresis and image analysis, authors did a comparative proteomic analysis with prefrontal cortex tissues of 17 suicide victims and 9 controls. Authors were able to identify five protein spots to differ in intensities between the two groups.

Journal: Journal of Biochemical and Biophysical Methods, June 10 [Epub March 14]
Title: A DIGE-based approach to study interacting proteins
Authors: A Lyakhovich; F Canals; M Nosov; J Surralles
Authors applied difference in-gel electrophoresis technique on native gel electrophoresis to study protein-protein interactions. As a proof of principle, they use an in vitro interaction model between p53 and HDM2 proteins and showed interaction of the proteins using fluorescently labeled p53- or HDM2- immunoprecipitation pellets.

Journal: Chemical Communications, June 7 [Epub March 2]
Title: CILAT – a new reagent for quantitative proteomics
Authors: S Li, D Zeng
Authors report the development of a new reagent, cleavable isobaric labeled affinity tag, for quantitative proteomics. According to them, CILAT is an improvement over current ICAT and iTRAQ methods.

Journal: Analytica Chimica Acta, June 5 [Epub April 27]
Title: Assessing the statistical validity of proteomics based biomarkers
Authors: S Smit; MJ van Breemen; HC Hoefsloot; AK Smilde; JM Aerts; CG de Koster;
Authors combined permutation tests, and single- and double-cross-validation to form a statistical basis for biomarker discovery. They say the strategy is “especially suited for the low-samples-to-variables-ratio (undersampling) case, as is often encountered in proteomics and metabolomics studies.”

Journal: Annals of Biomedical Engineering, June 2007 [Epub April 26]
Title: chip artifact CORRECTion (caCORRECT): A bioinformatics system for quality assurance of genomics and proteomics array data
Authors: TH Stokes; RA Moffitt; JH Phan; MD Wang
Authors report a web-based bioinformatics tool, caCORRECT, or chip artifact detection, analysis, and CORRECTion, which removes systematic artifact noises commonly observed in microarray gene expression data

Journal: Journal of Cancer Research and Clinical Oncology, June [Epub Jan. 12]
Title: A glycoproteome database of normal human liver tissue
Authors: HJ Zhou; Yk Liu; JF Chui; QL Sun; WJ Lu; K Guo; H Jin; LM Wei; PY Yang
Authors set out to construct the glycoprotein profile and a database of normal human liver tissue. Proteins were extracted from normal human liver tissue then subjected to 2D electrophoresis. 2D electrophoresis gels were stained according to methods of multiplexed proteomics technology, and glycoprotein spots were excised from 2D electrophoresis gel, then characterized by MALDI-TOF MS.

Journal: Proteomics, June
Title: iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing
Authors: J Lengqvist; K Uhlen; J Lehtio
Authors demonstrate the compatibility of pH gradient isolectric focusing with iTRAQ isotope labeling for relative quantitation and validation of sequence matches from database searching.

Journal: Molecular & Cellular Proteomics, May 28 [Epub ahead of print]
Title: Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy
Authors: BM Balgley; T Laudeman; L Yang; T Song; CS Lee
Authors conducted a survey of four MS/MS peptide identification search algorithms, Mascot, OMSSA, Sequest, and X!Tandem. They report that there is little difference in the output of the algorithms as long as consistent scoring procedures are applied. Results also show that some commonly used scoring procedures may lead to excessive false discovery rates. Authors propose an alternative method for determining an optimal cutoff threshold.

Journal: Molecular & Cellular Proteomics, May 28 [Epub ahead of print]
Title: The implications of proteolytic background for shotgun proteomics
Authors: P Picotti; R Aebersold; B Domon
Authors test the assumption that when analyzing complex peptide mixtures by LC-MS/MS, each protein present in a sample reproducibly and predictably generates a relatively small number of peptides that can be identified by MS. They used a targeted peptide sequence strategy, using inclusion lists to trigger peptide fragmentation attempts, and found that the number of peptides observed from a single protein is “at least one order of magnitude greater than previously assumed. This unexpected complexity of proteomic samples implies substantial technical challenges, explains some perplexing results in the proteomic literature, and prompts the need for developing alternative experimental strategies for the rapid and comprehensive analysis of proteomes,” according to the abstract.

Journal: Journal of Proteome Research, May 27 [Epub ahead of print]
Title: Optimization of mass spectrometry-compatible surfactants for shotgun proteomics
Authors: EI Chen; D Cociorva; JL Norris; JR Yates
Authors conducted a study optimizing and comparing trypsin digestion strategies for peptide/protein identifications by muLC-MS/MS with or without MS compatible detergents in mixed organic-aqueous and aqueous systems. Their results show that protein digestion schemes using MS-compatible detergents generate “quantitative as well as qualitative changes in observed peptide identifications, which lead to increased protein identifications overall and potentially increased identification of low-abundance proteins,” according to the abstract.

Journal: Electrophoresis, May 22 [Epub ahead of print]
Title: Interrogation of MS/MS search data with a pI filter algorithm to increase protein identification success
Authors: NC Uwaje; NS Mueller; G Maccarrone; CW Turck
Authors describe a filtering algorithm based on the comparison of the experimental and theoretical isoelectric point to validate peptide identifications by MS/MS data search engines.

Journal: Journal of Chromatography A, May 18, [Epub March 19]
Title: Restricted-access material-based high-molecular-weight protein depletion couple on-line with nano-liquid chromatography-mass spectrometry for proteomics applications
Authors: L Rieux; R Bischoff; E Verpoorte; HA Niederlander
Authors developed and characterized a set-up for multidimensional nanoLC-MS with three columns coupled on-line. The purpose was to devise a method for separate high-abundant from low-abundant proteins, especially albumin. The authors say that up to 99.7 percent of albumin would be removed over a 1-mm-I.D. restricted-access-material cartridge. “The set-up proved to be robust and was used for about 750 analyses without exchanging one of the columns. Flexibility with respect to the stationary phase material in the sample preparation cartridge allows for other separation modes to be applied as well,” according to the abstract.

Journal: Bioinformatics, May 17 [Epub ahead of print]
Title: Probability-based pattern recognition and statistical framework for randomization; Modeling tandem mass spectrum/peptide sequence false match frequencies
Authors: J Feng; DQ Naiman; B Cooper
Authors designed an unsupervised pattern recognition algorithm “for detecting patterns with various lengths from large sequence datasets,” according to the abstract. A Monte Carlo sampling algorithm was used to create decoy databases using patterns found in a protein sequence database. Searching the decoy databases led to the prediction of false positive rates for spectrum/peptide sequence matches.

Journal: Journal of Proteome Research, May 16 [Epub ahead of print]
Title: Enhanced a(1) fragmentation for dimethylated proteins and its applications for N-terminal identification and comparative protein quantitation
Authors: JL Hsu; SH Chen; DT Li; FK Shi
Authors developed a dimethyl labeling method at the protein level to assist the fragmentation of intact proteins using a Q-TOF MS. According to the authors, the method is useful in confirming proteolytic sites located at the N-terminus of proteins and can be incorporated with stable isotopes for “comparative profiling at the protein level, in which the heavily labeled and lightly labeled a1 ions were generated from the corresponding proteins upon high-voltage collisions in a broad mass region that covered all of the charge states of the proteins.”

Journal: Analytical Chemistry, May 15 [Epub April 19]
Title: Probability model for assessing proteins assembled from peptide sequences inferred from tandem mass spectrometry data
Authors: J Feng; DQ Naiman; B Cooper
Authors describe a probability model for determining the likelihood that peptides are correctly assigned to proteins. The model derives consistent probability estimates for assembled proteins. Probability scores make it easier to identify proteins in complex samples and accurately estimate false-positive rates, according to the abstract.

Journal: Analytical Chemistry, May 15, [Epub April 19]
Title: Implementation of electron-transfer dissociation on a hybrid linear ion trap-Orbitrap mass spectrometer
Authors: GC McAlister; D Phanstiel; DM Good; WT Berggren, JJ Coon
Authors describe the use of a hybrid quadruple linear ion trap Orbitrap MS for electron-transfer dissociation for peptide and protein characterization. The method utilizes pulsed, dual electrospray ion sources and requires minimal instrument modification, according to the abstract. Switching between cation and reagent anion injection schemes is automated, and ion/ion reactions are conducted within the linear ion trap.

Journal: Bioinformatics, May 11 [Epub ahead of print]
Title: Data reduction of isotope-resolved LC-MS Spectra
Authors: P Du, R Sudha; MB Prystowsky; RH Angeletti
Authors present a new algorithm, LCMS-2D, for data reduction of LC-MS proteomics data. The authors say that the algorithm can reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to a list of peptide masses.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.