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Recent Research Papers of Note in Proteomics: Aug 7, 2008

Journal: Analytical Chemistry, Aug. 5 [Epub ahead of print]
Title: Comparison of two-dimensional fractionation techniques for shotgun proteomics
Authors: JA Dowell; DC Frost; J Zhang; L Li
Authors set out to compare the relative separation efficiencies of 2D methodologies using low microgram sample quantities by fractionating microgram quantities of E. coli protein extract by seven different methods. Reversed-phase high pressure liquid chromatography, gel electrophoresis, or strong cation exchange was done for the first dimension of separation. The second dimension was performed by standard reversed-phase capillary HPLC coupled to an electrospray ionization quadrupole TOF-MS for tandem mass spectrometric analysis. Performance and fractionation efficiencies for each technique were evaluated by comparing the total number of proteins identified by each method. The authors report that protein-level RP-HPLC and the high-pH RP-HPLC peptide-level separations did the best, identifying 281 and 266 proteins, respectively.

Journal: Molecular & Cellular Proteomics, Aug. 3 [Epub ahead of print]
Title: Quantitative serum proteomics from surface plasmon resonance imaging
Authors: CG Lausted; Z Hu; LE Hood
Authors describe a high-throughput, label-free method for serum analysis using surface plasmon resonance imaging of antibody microarrays. The system was validated by measuring the concentrations of four serum proteins using part of a 792-feature microarray.

Journal: Rapid Communications in Mass Spectometry: RCM, Aug. 1 [Epub ahead of print]
Title: Imaging mass spectrometry using peptide isoelectic focusing
Authors: AR Vaezzadeh; J Simicevic; A Chauvet; P Francois; CG Zimmermann-Ivol; P Lescuyer; JP Deshusses; DF Hochstrasser
Authors combined imaging mass spectrometry and immobilized pH gradient-isoeletric focusing. The approach is based on the separation of shotgun-produced peptides by IPG-IEF. The peptides are then transferred by capillarity to a capture membrane, which is scanned by mass spectrometry, generating MS images. The authors also applied the pipeline for differential comparison of the membrane proteome of two different strains of Staphylococcus aureus bacteria.

Journal: Molecular & Cellular Proteomics, July 31 [Epub ahead of print]
Title: A gene-centric human protein atlas for expression profiles based on antibodies
Authors: L Berglund; E Björling; P Oksvold; L Fagerberg; A Asplund; C Al-Khalili Szigyarto; A Persson; J Ottosson; H Wernérus; P Nilsson; E Lundberg; A Sivertsson; S Navani; K Weter; C Kampf; S Hober; F Pontén; M Uhlén
Authors report a new version 4.0 of the Human Protein Atlas, developed in a gene-centric manner, which includes all human genes and splice variants predicted from genome efforts “together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide and proteins domains and new plots showing the uniqueness … of every fraction of each protein toward all other human proteins,” according to the paper’s abstract.

Journal: Molecular & Cellular Proteomics, July 30 [Epub ahead of print]
Title: Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results
Authors: K Helsens; E Timmerman; J Vandekerckhove; M Gevaert; L Martens
Presented is a novel tool to address the “expanding diversity in available proteomics technologies” meant to remove false-positive peptide identifications, the authors say in the abstract. The tool, called Peptizer, makes use of “pluggable assumptions” and includes a graphical user-interface for efficient manual validation of suspect identifications for sensitivity recovery.

Journal: Molecular & Cellular Proteomics, July 29, [Epub ahead of print]
Title: Antibodypedia – a portal for sharing antibody and antigen validation data
Authors: E Björling; M Uhlén
A new publicly available portal, called Antibodypedia, is described. The portal is meant to be a standardized system for sharing validation data about publicly available antibodies, and to allow antibody providers and users to contribute and edit experimental evidence data, including data on the antigen.

Journal: Journal of Proteome Research, July 29 [Epub ahead of print]
Title: Optimizing sample handling for urinary proteomics
Authors: RS Lee; F Monigatti; AC Briscoe; Z Waldon; MR Freeman; H Steen
Authors demonstrate that the method of protein extraction, length of handling at room temperature, and repetitive freeze-thaw cycles do not seem to alter the urinary proteome at the peptide or protein level in such a way as to degrade information obtainable by mass spectrometry.

Journal: Journal of Proteome Research, July 25 [Epub ahead of print]
Title: Automated SPR-LC-MS/MS system for protein interaction analysis
Authors: T Hayano; Y Yamauchi; K Asano; T Tsujimura; S Hashimoto; T Isobe; N Takahashi
Described is a new automated system for the analysis of protein complexes, integrating a surface plasmon resonance biosensor with highly sensitive nanoflow liquid chromatography-tandem mass spectrometry. A His-tagged protein, tagged also with FLAG and biotinylated sequences, was expressed in mammalian cells. The sample protein was purified using the His tag from the cell lysate, then applied to an SPR biosensor, and captured on the sensor chip.
The automated SPR-LC-MS/MS was done. In the first phase, the on-chip protein complex was purified using the FLAG and biotinylated tags, followed by on-chip protease digestion of the complex, and finally online nanoflow LC-MS/MS analysis of the resulting peptide fragments for protein identification.

Journal: Proteomics, July 24 [Epub ahead of print]
Title: Direct visualization of fluorescent signals in protein gels using a backlit blue light plate
Authors: SY Wu; LT Chin; LM Chen; HM Chen
Described is a new setup using a blacklit blue light plate for illuminating fluorescently stained protein gels. The method uses Snell’s law and allows for the direct visualization of signals in protein gels without the use of filters or filter glasses.

Journal: Proteomics, July 24 [Epub ahead of print]
Title: Application of a peptide-based PF2D platform for quantitative proteomics in disease biomarker discovery
Authors: HJ Lee; MJ Kang; EY Lee; SY Cho; H Kim; YK Paik
Authors used a peptide-based 2D liquid phase fractionation system for the quantitative analysis of hepatocellular carcinoma. They report that 2D liquid maps of peptide specimens had better resolution than those of proteins resulting in the identification of differentially expressed proteins.

Journal: BMC Bioinformatics, July 21 [Epub ahead of print]
Title: PatternLab for proteomics: a tool for differential shotgun proteomics
Authors: PC Carvalho; JS Fischer; EI Chen; JR Yates; VC Barbosa
The program, PatternLab, implements existing strategies while adding two new methods to pinpoint differences in protein profiles.

Journal: Molecular & Cellular Proteomics, July 20 [Epub ahead of print]
Title: Significance analysis of spectral count data in label-free shotgun proteomics
Authors: H Choi; D Fermin; AI Nesvizhskii
Authors present a statistical framework called QSpec for the significance analysis of differential expression “with extension to a variety of experimental design factors and adjustments for protein properties,” according to the paper’s abstract.

Journal: Molecular & Cellular Proteomics, July 18 [Epub ahead of print]
Title: MRMer: An interactive open-source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.
Authors: DB Martin; T Holzman; D May; A Peterson; A Eastham; J Eng; M McIntosh
The interactive software platform MRMer parses and extracts information from mass spec files encoded in the platform-independent mzXML data format. The platform “extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1,000 precursor-product pairs,” the authors said in the paper’s abstract, and results are easily output for quantitative comparison of consecutive runs. MRMer also incorporates features permitting quantitative analysis experiments including heavy and light isotopic peptide pairs.

Journal: Journal of Proteome Research, July 17 [Epub ahead of print]
Title: DirecTag: Accurate sequence tags from peptide MS/MS through statistical scoring
Authors: DL Tabb; ZQ Ma; DB Martin; AJ Ham; MC Chambers
Described is DirecTag, an open-source algorithm to infer partial sequence tags directly from observed fragment ions. The authors say in the paper’s abstract that the algorithm is unique “in its implementation of three separate scoring systems to evaluate each tag on the basis of peak intensity, m/z fidelity, and complementarity.” In data sets from several types of mass spectrometers, DirecTag reproducibly exceeded the accuracy and speed of InsPecT and GutenTag.

Journal: Bioinformatics, July 16 [Epub ahead of print]
Title: The Protein Information and Property Explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.
Authors: H Ramos; P Shannon; R Aebersold
The Protein Information and Property Explorer, or PIPE, allows for the acquisition of functional annotations for the litany of proteins resulting from mass spectrometry experiments and for the exploration of the enrichment of the list with respect functional classes. PIPE is interoperable with the Firegoose and the Gaggle integration software tools, “permitting wide-ranging data exploration and analysis,” according to the paper’s abstract.

Journal: Journal of Proteome Research, July 15, [Epub ahead of print]
Title: A mouse model repository for cancer biomarker discovery
Authors: KS Kelly-Spratt; AE Kasarda; M Igra; CJ Kemp
According to the authors, inbred mouse models of cancer “recapitulate many critical features of human cancer, while eliminating sources of environmental and genetic variability.” They describe the creation of a repository containing tumor, plasma, urine, and other tissues from 10 different mouse models of human cancer, including two breast, two lung, two prostate, two gastrointestinal, one ovarian, and one skin tumor model.

Journal: Analytical Chemistry, July 11 [Epub ahead of print]
Title: Strategy for determination of in vitro protein acetylation sites by using isotope-labeled acetyl coenzyme A and liquid chromatography-mass spectrometry.
Authors: HY Wu; FY Huang; YC Chang; MC Hsieh; PC Liao
Authors propose a strategy for determining in vitro acetylation sites of proteins by tracing isotope-labeled acetyl groups using mass spectrometry. Isotope-labeled and unlabeled acetyl groups transferred onto the substrates in vitro result in a specific mass difference that measurable by MS analysis and used for localization of potential acetylated peptide signals. MS/MS experiments facilitate the identification of acetylation sites on those selected signals.

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