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Recent Research Papers of Note: Sep 10, 2009

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Journal: Electrophoresis, September
Title: The consequences of sample pooling in proteomics: an empirical study
Authors: AP Diz; M Turebano; DO Skibinski

The authors study three issues that may determine the success of a sample pooling approach in proteomics and "provide evidence that (i) the protein expression in a pool matches the mean expression of the individuals making up the pool for the majority of proteins, although for some proteins the pool expression is different; (ii) the biological variance between pools is reduced compared with that between individuals, as predicted in theory, but this reduction is not as large as expected. A practical consequence of this is that power could be reduced; (iii) proteins detectable in individual samples are usually but not always visible when samples are pooled,” according to the abstract. They conclude that the pooling of samples is a valid approach in proteomics and a "potentially valuable procedure, but consideration should be given to these issues in experimental design."


Journal: Proteomics, Aug. 31 [Epub ahead of print]
Title: A MS data search method for improve N15-labeled protein identification
Authors: Y Zhang; C Webhofer; S Reckow; MD Filou; G Maccarrone; CW Turck

In the abstract, the authors say that stable isotope-labeling strategies combined with mass spectrometry is an "important" tool for biomarker discovery, but stable isotope incorporation rates in metabolic labeling experiments "using mammalian organisms usually do not reach 100 percent. As a consequence, protein identifications in N15database searches have poor success rates." Here, they report a strategy that "significantly" improves the number of N15-labeled protein identifications and results.


Journal: Proteomics, Aug. 28 [Epub ahead of print]
Title: 2D-PAGE and MS analysis of proteins from formalin-fixed, paraffin-embedded tissues
Authors: MF Addis; A Tanca; D Pagnozzi; S Rocca; S Uzzau
According to the abstract, 2D PAGE protein maps with "satisfactory proteomic information and comparability to fresh tissues" have never been described. In their study, the authors report 2D PAGE separation and MS identification of full-length proteins extracted from FFPE skeletal muscle tissue. Up to 250 spots were "clearly detected" in 2D maps of proteins from FFPE tissue following standard mass-compatible silver staining. They say that the study "provides evidence that, when adequately extracted, full-length proteins from FFPE tissues might be suitable for 2-D PAGE-MS analysis, allowing differential proteomic studies on the vast existing archives of healthy and pathological-fixed tissues."


Journal: Cell, Aug. 21
Title: Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Authors: P Picotti; B Bodenmiller; LN Mueller; B Domon; R Aebersold

Described is the application of a targeted proteomics approach based on selected-reaction monitoring to detect and quantify proteins expressed to a concentration below 50 copies per cell in total S. cerevisiae digests. They illustrate the power of the technique by the "consistent and fast measurement of a network of proteins spanning the entire abundance range over a growth time course of S. cerevisiae transiting through a series of metabolic phases," according to the abstract.


Journal: Bioinformatics, Aug. 18 [Epub ahead of print]
Title: Improving peptide identification with single-stage mass spectrum peaks
Authors: Z He; W Yu

Described is a method for improving MS/MS spectral identification by database searching in shotgun proteomics. The authors show that single-stage MS data, which is complementary to MS/MS data, can be used to re-rank peptide-spectrum matches. "The proposed method explores a linear combination of scores between MS and MS/MS data to perform re-ranking," according to the abstract.

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Journal: Journal of Proteome Research, Aug. 14 [Epub ahead of print]
Title: False discovery rates of protein identifications: a strike against the two-peptide rule
Authors: N Gupta; PA Pevzner

According to the authors, most proteomics studies infer proteins containing two or more peptides as reliable protein identifications, but in an evaluation of this "two-peptide" rule, they found that this approach "reduces the number of protein identifications in the target database more significantly than in the decoy database and results in increased false discovery rates, compared to the case when single-hit proteins are not discarded." As a result, they call for abandoning the "two-peptide" rule. Instead, “protein identifications should be subject to the estimation of error rates, as in the case with peptide identifications.”


Journal: Molecular & Cellular Proteomics, Aug. 14 [Epub ahead of print]
Title: Report: A community standard format for the representation of protein affinity reagents
Authors: DE Gloriam; S Orchard; D Bertinetti, et al

The paper calls for the adoption of PSI-Par as a global community standard format for the exchange of protein affinity reagent data. PSI-PAR is maintained by the Human Proteome Organization's Proteomics Standards Initiative and because it is built on a mature and widely accepted proteomics standard format, PSI-MI, it has the advantage of being thoroughly tested, has software tools that already have been developed, and reduced maintenance [See related story this issue].


Journal: Analytical Biochemistry, Aug. 11 [Epub ahead of print]
Title: A label-free mass spectrometry method for the quantification of protein isotopes
Authors: RD Winefield; TD Williams; RH Himes

Described is a label-free technique for analyzing products from related genes. "This approach enables the invariant tryptic peptide sequences within the family to serve as 'built-in' internal standards and the isotype-specific peptide sequences to report the amount of the various isotypes," according to the abstract.


Journal: Journal of Proteome Research, Aug. 11 [Epub ahead of print]
Title: High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all
Authors: T Köcher, P Pichler; M Schutzbier; C Stingl; A Kaul; G Hasenfuss; N Teucher; J Penninger; K Mechtler

Described is a method for "sensitive and accurate" protein identification, as well as isobaric labeling-based quantitative proteomics, especially iTRAQ labeling on ion traps and hybrid mass spectrometers containing an ion trap [See PM 08/20//09].


Journal: Journal of Proteomics, Aug. 8 [Epub ahead of print]
Title: Pre-analytical factors in clinical proteomics investigations: Impact of ex vivo protein modifications for multiple sclerosis biomarker discovery
Authors: D Pieragostino; F Petrucci; P DelBoccio; D Mantini; A Lugaresi; S Tiberio; M Onofrj; D Gambi; P Sacchetta; C Di Ilio; G Federici; A Urbani

Described is a "systematic evaluation of sample storage and sampling conditions for proteomics investigations," according to the abstract. The authors say that they have developed and validated a MALDI-TOF-MS protein profiling method for the exploration of the low protein-molecular-weight region of serum samples.


Journal: Cell Stem Cell, Aug. 7
Title: Unraveling the human embryonic stem cell phosphoproteome
Authors: AP Hutchins; P Robson

The human embryonic stem cell is well described but only minimal proteome characterization is currently available, according to the abstract. The study describes the hESC phosphoproteome and its changes upon differentiation.

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