Systematic errors in peptide and protein identification and quantification by modified peptides

The principle of shotgun proteomics is to use peptide mass spectra in order to identify corresponding sequences in a protein database. The quality of peptide and protein identification and quantification critically depends on the sensitivity and specificity of this assignment process. Many peptides in proteomic samples carry biochemical modifications, and a large fraction of unassigned spectra arise from modified peptides. Spectra derived from modified peptides can erroneously be assigned to wrong amino acid sequences. However, the impact of this problem on proteomic data has not yet been investigated systematically. Here we use combinations of different database searches to show that modified peptides can be responsible for 20-50 % of false positive identifications in deep proteomic datasets. These false positive hits are particularly problematic as they have significantly higher scores and higher intensities than other false positive matches. Furthermore, these wrong peptide assignments lead to hundreds of false protein identifications and systematic biases in protein quantification. We devise a "cleaned search" strategy to address this problem and show that this considerably improves the sensitivity and specificity of proteomic data. In summary, we show that modified peptides cause systematic errors in peptide and protein identification and quantification and should therefore be considered to further improve the quality of proteomic data annotation

Social Comparisons, Social Support, and Self-Perceptions in Group Exercise for People With Parkinson's Disease

People with Parkinson's disease (PD) may experience declining function and limited interaction with others with PD. Group exercise provides opportunities for physical accomplishment and social support, as well as potential social challenges. We used interpretative phenomenological analysis to examine experiences of social comparison, social support, and self-perceptions of 20 people with PD in group exercise. Participants experienced (a) reticence evolving to inspiration, (b) anxiety relief through camaraderie and breaking taboos, and (c) maintaining athletic identity through participating and helping others. Practical implications include facilitating a safe space and support to alleviate anxiety and sustain participation

Keeping the proportions of protein complex components in check

How do cells maintain relative proportions of protein complex components? Advances in quantitative, genome-wide measurements have begun to shed light onto the roles of protein synthesis and degradation in establishing the precise proportions in living cells: on the one hand, ribosome profiling studies indicate that proteins are already produced in the correct relative proportions. On the other hand, proteomic studies found that many complexes contain subunits that are made in excess and subsequently degraded. Here, we discuss these seemingly contradictory findings, emerging principles, and remaining open questions. We conclude that establishing precise protein levels involves both coordinated synthesis and post-translational fine-tuning via protein degradation

A Novel Hypothesis on the Sensitivity of the Fecal Occult Blood Test Results of a Joint Analysis of 3 Randomized Controlled Trials

BACKGROUND: Estimates of the fecal occult blood test (FOBT) (Hemoccult II) sensitivity differed widely between screening trials and led to divergent conclusions on the effects of FOBT screening. We used microsimulation modeling to estimate a preclinical colorectal cancer (CRC) duration and sensitivity for unrehydrated FOBT from the data of 3 randomized controlled trials of Minnesota, Nottingham, and Funen. In addition to 2 usual hypotheses on the sensitivity of FOBT, we tested a novel hypothesis where sensitivity is linked to the stage of clinical diagnosis in the situation without screening. METHODS: We used the MIS-CAN-Colon microsimulation model to estimate sensitivity and duration, accounting for differences between the trials in demography, background incidence, and trial design. We tested 3 hypotheses for FOBT sensitivity: sensitivity is the same for all preclinical CRC stages, sensitivity increases with each stage, and sensitivity is higher for the stage in which the cancer would have been diagnosed in the absence of screening than for earlier stages. Goodness-of-fit was evaluated by comparing expected and observed rates of screen-detected and interval CRC. RESULTS: The hypothesis with a higher sensitivity in the stage of clinical diagnosis gave the best fit. Under this hypothesis, sensitivity of FOBT was 51% in the stage of clinical diagnosis and 19% in earlier stages. The average duration of preclinical CRC was estimated at 6.7 years. CONCLUSIONS: Our analysis corroborated a long duration of preclinical CRC, with FOBT most sensitive in the stage of clinical diagnosis. Cancer 2009;115:2410-9. (C) 2009 American Cancer Society

Interaction of synchronized dynamics in cortical and subcortical circuits in Parkinson’s disease

poster abstractParkinson’s disease pathophysiology is marked by increased oscillatory and synchronous activity in the beta frequency band in cortical and basal ganglia circuits. This study explores the functional connections between synchronized dynamics of cortical areas and dynamics of subcortical areas in Parkinson’s disease. We simultaneously recorded neuronal units (spikes) and local field potentials (LFP) from subthalamic nucleus (STN), and electroencephalograms (EEGs) from the scalp in parkinsonian patients and analyzed the correlation between the time-courses of the spike-LFP synchronization and inter-electrode EEG synchronization. We found the (noninvasively obtained) time-course of the synchrony strength between EEG electrodes and the (invasively obtained) time-course of the synchrony between spiking unit and LFP in STN to be weakly, but significantly correlated with each other. This correlation is largest for the bilateral motor EEG synchronization followed by bilateral frontal EEG synchronization. Our observations suggest that there may be multiple functional modes by which the cortical and basal ganglia circuits interact with each other in Parkinson’s disease: not only synchronization may be observed between some areas in cortex and the basal ganglia, but also synchronization within cortex and within basal ganglia may be related, suggesting potentially more global way of functional interaction. More coherent dynamics in one brain region may modulate or activate the dynamics of another brain region in a more powerful way causing correlations between changes in synchrony strength in both regions

Quantitative GTPase affinity purification identifies Rho family protein interaction partners

Although Rho GTPases are essential molecular switches involved in many cellular processes, an unbiased experimental comparison of their interaction partners was not yet performed. Here, we develop quantitative GTPase affinity purification (qGAP) to systematically identify interaction partners of six Rho GTPases (Cdc42, Rac1, RhoA, RhoB, RhoC, RhoD) depending on their nucleotide loading state. The method works with cell line or tissue-derived protein lysates in combination with SILAC-based or label free quantification, respectively. We demonstrate that qGAP identifies known and novel binding partners that can be validated in an independent assay. Our interaction network for six Rho GTPases contains many novel binding partners, reveals highly promiscuous interaction of several effectors and mirrors evolutionary relationships among Rho GTPases

TERC polymorphisms are associated both with susceptibility to colorectal cancer and with longer telomeres.

Shorter telomeres have been associated with increased risk of malignancy, including colorectal cancer (CRC). Telomere length is heritable and may be an intermediate phenotype linked to genetic susceptibility to CRC