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“In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples

of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled

quantitation.”
“Purpose: We assessed whether the impact of partial nephrectomy and radical nephrectomy on overall mortality differed by patient age in a Medicare population undergoing surgery for T1a renal cell carcinoma.

Materials and Methods: Using linked SEER (Surveillance, Epidemiology and End Results)-Medicare data, we identified patients older than 66 years who underwent partial nephrectomy or radical nephrectomy for T1a (4 cm or smaller) renal cell carcinoma from 1995 to 2007. The effects of procedure type on overall mortality by age were assessed using time dependent Cox proportional hazards models adjusted by propensity score based weighting.

Results: A total of 5,496 patients (mean age 74.2 +/- 5.6 years, 55.9% male) who underwent partial nephrectomy (1,665; 30.3%) or radical nephrectomy (3,831; 69.7%) for 4 cm or smaller renal cell carcinoma (mean tumor size 2.8 +/- 0.9 cm) were identified. After adjustment, a statistically significant survival benefit for partial nephrectomy compared to radical nephrectomy was observed at 1 year (age 68, HR 1.6, CI 1.2-2.3; age 75, HR 1.5, CI 1.1-1.9; age 85, HR 1.7, CI 1.1-2.5) and 3 years (age 68, HR 1.4, CI 1.03-2.0; age 75, HR 1.3, CI 1.1-1.6; age 85, HR 1.5, CI 1.02-2.3), while these trends became insignificant in patients

younger than 68 and older than 85 years. However, the survival benefit decreased with time, and little significant benefit with partial nephrectomy was observed at 5 and 10 years after surgery regardless of age (66 years or older).

Conclusions: Lacking strong evidence regarding a long-term survival benefit, the decision to perform partial nephrectomy in elderly patients should be individualized, and placed in the context of baseline renal function, expected surgical morbidity and competing risks to survival.”
“Phosphorylation of proteins is one of the most prominent PTMs and for instance a key regulator of signal transduction. In order to improve our understanding of cellular phosphorylation events, considerable effort has been devoted to improving the analysis of phosphorylation by MS-based proteomics.