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Recent Research Papers of Note: Feb 5, 2010

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Journal: Analytical Chemistry, Feb.1
Title: Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase TiO2-reversed phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer
Authors: R Raijmakers; K Krajczek; AP de Jong; S Mohammed; AJ Heck

The authors recently introduced a method to facilitate the analysis of phosphopeptides by performing automated online TiO2 enrichment of phosphopeptides prior to MS analysis. In the current study, they showed that the so-called "phosphochip" can enrich large numbers of phosphopeptides from complex cellular lysates, "which can be more readily identified when coupled to a higher resolution quadrupole time-of-flight mass spectrometer," according to the abstract. Using the phosphochip-Q-TOF setup to explore the phosphoproteome of non-stimulated primary human leukoctyes, they identified, 1,012 unique phosphopeptides corresponding to 960 different phosphorylation sites, "providing for the first time an overview of the phosphoproteome of these important circulating white blood cells."


Journal: Rapid Communications in Mass Spectrometry: RCM, February
Title: MSQ: a tool for quantification of proteomics data generated by a liquid chromatography/matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry-based targeted quantitative proteomics platform.
Authors: JH Oh; S Pan; J Zhang; J Gao

The authors have developed software called Mass Spectrometry-based Quantification, or MSQ, to establish an LC-MALDI-TOF/TOF-based targeted quantitative proteomics pipeline. MSQ can be used to automate the quantification and identification of targeted peptides and proteins by MALDI-TOF/TOF. Used for detecting a selected group of targeted peptides in pooled human cerebrospinal fluid from patients with Alzheimer's disease compared to age-matched control, MSQ achieved results that were in "good agreement with results calculated manually," according to the abstract.


Journal: The Protein Journal, Jan. 22 [Epub ahead of print]
Title: Shotgun mass spectrometry workflow combining IEF and LC-MALDI-TOF/TOF
Authors: G Maccarone; CW Turck; D Martins de Souza

Presented is a high-throughput shotgun mass spec workflow using a bidimensional peptide fractionation procedure consisting of isoelectric focusing and RP-HPLC prior to MS analysis for optimizing peptide separation and protein identification.


Journal: Analytical Chemistry, Jan. 21 [Epub ahead of print]
Title: Development of mass spectrometry-based shotgun method for proteome analysis of 500 to 5,000 cancer cells
Authors: N Wang; M Xu; P Wang; L Li

Described is a shotgun proteomic analysis method for protein identification from 500 to 5,000 cells. Sample preparation was done in one tube, using a surfactant for cell lysis, followed by acetone precipitation of the proteins. The resulting protein pellet was washed with cold acetone, and the pellet was solubilized in NH4HCO3. The digest was analyzed by nanoLC-Q-TOF mass spectrometry, following tryptic digestion.


Journal: Journal of Proteome Research, Jan. 20 [Epub ahead of print]
Title: Single-step procedure for the isolation of proteins at near-native conditions from mammalian tissue for proteomic analysis on antibody microarrays
Authors: MS Alhamdani; C Schröder; J Werner; N Giese; A Bauer; JD Hoheisel

In the abstract, the authors said that though microarrays are "an evolving and promising methodology in proteomics, the issue of protein extraction from tissues for this kind of analysis has never been addressed." Described is a "single-step extraction buffer for the isolation of proteins from mammalian tissues under native conditions in an effective and reproducible manner."


Journal: Analytical Chemistry, Jan. 15
Title: Affinity-trap polyacrylamide gel electrophoresis: a novel method of capturing specific proteins by electro-transfer
Authors: C Awada; T Sato; T Takao

According to the abstract, the affinity capture method is based on the orthogonal electro-transfer of proteins separated by "ordinary polyacrylamide gel electrophoresis to a ligand-coupled polyacrylamide gel, which is placed under the PAGE gel." Upon electro-transfer, the proteins orthogonally migrate from the PAGE to the Li-PAG. During this migration, proteins that specifically interact with a ligand can be transiently trapped in the Li-PAG. Those that do not interact with a ligand pass through it. "This method permits the separation of the proteins that can specifically interact with a ligand, even when present in a complex mixture," according to the abstract.


Journal: Analytical Chemistry, Jan. 14 [Epub ahead of print]
Title: Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80 kDa
Authors: A Vellaichamy; JC Tran; AD Catherman; JE Lee; JF Kellie; SM Sweet; L Zamdborg; PM Thomas; DR Ahlf; KR Durbin; GA Valaskovic; NL Kelleher

Reported are "robust" protocols for online LC-MS "to drive high-throughput top-down proteomics in a fashion similar to that of bottom-up proteomics," according to the abstract. ”Comparative work on protein standards showed that a polymeric stationary phase led to superior sensitivity over a silica-based medium in reversed-phase nanocapillary LC, with detection of proteins [greater than] 50 kDa routinely accomplished in the linear ion trap of a hybrid Fourier transform mass spectrometer," the authors added.


Journal: Proteomics, Jan. 13 [Epub ahead of print]
Title: Semi-automatic tool to describe, store, and compare proteomics experiments based on MIAPE compliant reports
Authors: S Martínex-Bartolomé; JA Medina-Aunon; AR Jones; JP Albar

To promote the implementation of standard reporting guidelines, the authors have developed a web tool that helps generate and store Minimum Information About a Proteomics Experiment, or MIAPE, compliant reports describing gel electrophoresis and MS-based experiments.


Journal: Journal of Proteome Research, Jan. 11 [Epub ahead of print]
Title: An LC-MS platform providing increased dynamic range for high-throughput proteomic studies
Authors: ES Baker; EA Livesay; DJ Orton; RJ Moore; WF Danielson; DC Prior; YM Ibrahim; BL Lamarche; AM Mayampurath; AA Schepmoes; DF Hopkins; K Tang; RD Smith; ME Belov

The authors evaluated a high-throughput approach and platform using 15-minute reversed-phase capillary liquid chromatography separations in conjunction with ion mobility spectrometry-mass spectrometry measurements for analyzing complex proteomics samples. They tested the separation quality of the short LC gradient by preparing a sample spiked with 20 reference peptides at varying concentrations into a tryptic digest of mouse blood plasma, and analyzed it with both an LC-FT MS platform and LC-IMS-TOF MS platform. The LC-FT MS system detected 13 out of 20 spiked peptides with a concentration greater than 100 ng/mL. "In contrast, the drift time selected mass spectra from the LC-IMS-TOF MS analyses yielded identifications for 19 of the 20 peptides with all spiking levels present," according to the abstract.