Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

We designed a 15-item neurologic examination stroke scale for use in acute stroke therapy trials. In a study of 24 stroke patients, interrater reliability for the scale was found to be high (mean kappa = 0.69), and test-retest reliability was also high (mean kappa = 0.66-0.77). Test-retest reliability did not differ significantly among a neurologist, a neurology house officer, a neurology nurse, or an emergency department nurse. The stroke scale validity was assessed by comparing the scale scores obtained prospectively on 65 acute stroke patients to the patients' infarction size as measured by computed tomography scan at 1 week and to the patients' clinical outcome as determined at 3 months. These correlations (scale-lesion size r = 0.68, scale-outcome r = 0.79) suggested acceptable examination and scale validity. Of the 15 test items, the most interrater reliable item (pupillary response) had low validity. Less reliable items such as upper or lower extremity motor function were more valid. We discuss methods for improving the reliability and validity of brief examination scales to be used in stroke therapy trials.

Measurements of acute cerebral infarction: a clinical examination scale.

The development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73, 57, 48, and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor blockade in 24 patients who objectively responded to therapy but subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase pathway. Together, these data suggest that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.

/pdf/detection-of-circulating-tumor-dna-in-early-and-late-stage-2x27qw0fo9.pdf

Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

Recent advances in next-generation DNA sequencing and proteomics provide an unprecedented ability to survey mRNA and protein abundances. Such proteome-wide surveys are illuminating the extent to which different aspects of gene expression help to regulate cellular protein abundances. Current data demonstrate a substantial role for regulatory processes occurring after mRNA is made - that is, post-transcriptional, translational and protein degradation regulation - in controlling steady-state protein abundances. Intriguing observations are also emerging in relation to cells following perturbation, single-cell studies and the apparent evolutionary conservation of protein and mRNA abundances. Here, we summarize current understanding of the major factors regulating protein expression.

/pdf/insights-into-the-regulation-of-protein-abundance-from-1nb4o968ef.pdf

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

The hypothesis that dopamine is important for reward has been proposed in a number of forms, each of which has been challenged. Normally, rewarding stimuli such as food, water, lateral hypothalamic brain stimulation and several drugs of abuse become ineffective as rewards in animals given performance-sparing doses of dopamine antagonists. Dopamine release in the nucleus accumbens has been linked to the efficacy of these unconditioned rewards, but dopamine release in a broader range of structures is implicated in the 'stamping-in' of memory that attaches motivational importance to otherwise neutral environmental stimuli.

Dopamine, learning and motivation

AFFECTIONS of the nervous system which result from inadequate nutrition have assumed an increasingly important position through the rapid accumulation of clinical, experimental, and pathological data. The artificial synthesis of a number of the components of the vitamin B complex has made available pure crystalline material in large amounts for clinical research, and thus a milestone in the history of these affections has been passed. It now seems appropriate to review and summarize the knowledge of these important substances. To evaluate the status of a nutritional deficiency in man is difficult. As a rule the patient induces his own disease and provides a deficiency that is not quantitatively measurable, but frequently clinical and laboratory evaluations are attempted. Both the laboratory method and the clinical method have certain advantages. Mice are not yet men and until they are the work coming -from the study of human beings is essential. Since the experience of investigators working with animals may often point the way for clinical research, we have interspersed in this review a few of the pertinent studies on the effect of nutritional deficiency on the nervous system of animals. A scheme for illustrating the multiple factors of the vitamin B complex is given in Fig. 1. To date the following portions of the vitamin B complex have been isolated and synthesized in amounts sufficient to allow for clinical trial: thiamin hydrochloride, nicotinic acid, riboflavin, and 2-methyl, 3-hydroxy, 4, 5-di (hydroxymethyl) pyridine. The deficiencies of these substances as they apply to the nervous system of man will be discussed briefly.

https://jnnp.bmj.com/content/jnnp/2/4/335.full.pdf

C. D. Aring

Papers

A critical review: vitamin b deficiency and nervous disease.