Noise filtering techniques for electrospray quadrupole time of flight mass spectra

AbstractThe sensitivity of protein identification by peptide sequencing using a nanoelectrospray ion source is limited by our ability to identify peptide ions in the mass spectrum. Their intensity must be higher than the chemical noise level to allow a rapid localization in the spectrum. Multiply-charged peptide ions on or below this level can only be found because their isotopic pattern is denser than that of the mostly singly-charged chemical background ions. However, to find peptides by looking for multiply-charged isotope clusters can be very timeconsuming and may lead to misassignments of the first isotope. Here we present a software-based method to increase the signal to noise ratio of ion signals in an electrospray spectrum. The software has two elements, one to reduce the noise level and a second to increase the intensity of ion peaks. Both methods together generate a spectrum in which the signal to noise ratio of ion signals is considerably improved. Peptide ions previously hidden in the chemical background are dismantled and can now be localized and selected for fragmentation. The method has been used successfully to identify low level proteins separated by one dimensional gel electrophoresis

A Neutrophil Proteomic Signature in Surgical Trauma Wounds

Non-healing wounds continue to be a clinical challenge for patients and medical staff. These wounds have a heterogeneous etiology, including diabetes and surgical trauma wounds. It is therefore important to decipher molecular signatures that reflect the macroscopic process of wound healing. To this end, we collected wound sponge dressings routinely used in vacuum assisted therapy after surgical trauma to generate wound-derived protein profiles via global mass spectrometry. We confidently identified 311 proteins in exudates. Among them were expected targets belonging to the immunoglobulin superfamily, complement, and skin-derived proteins, such as keratins. Next to several S100 proteins, chaperones, heat shock proteins, and immune modulators, the exudates presented a number of redox proteins as well as a discrete neutrophil proteomic signature, including for example cathepsin G, elastase, myeloperoxidase, CD66c, and lipocalin 2. We mapped over 200 post-translational modifications (PTMs; cysteine/methionine oxidation, tyrosine nitration, cysteine trioxidation) to the proteomic profile, for example, in peroxiredoxin 1. Investigating manually collected exudates, we confirmed presence of neutrophils and their products, such as microparticles and fragments containing myeloperoxidase and DNA. These data confirmed known and identified less known wound proteins and their PTMs, which may serve as resource for future studies on human wound healing

Bioactive hydrolysates from bovine blood globulins: Generation, characterisation, and in silico prediction of toxicity and allergenicity

peer-reviewedTwo protein fractions rich in γ-globulins (FI) and α- and β-globulins (FII) were generated from bovine blood and hydrolysed with the enzyme papain. The generated hydrolysates showed in vitro angiotensin-I-converting enzyme (ACE-I), renin, and dipeptidyl peptidase-IV (DPP-IV) inhibitory activities. A total of 626 and 2246 peptides were identified by LC-MS/MS from the 1 kDa fractions of FI and FII, and the potential toxicity and allergenicity of these peptides were assessed in silico using three independent predictive approaches. All of the peptides identified from the bioactive blood protein fractions FI and FII were predicted to be non-toxic. However, 72 peptides from FI and 492 peptides from FII were identified as potential allergens with at least two predictive approaches. Results suggested that papain hydrolysates of FI and FII contain potential allergenic peptides, and those products containing such hydrolysates should be labelled correctly in line with Food and Consumer legislation – Regulation (EU) No.1169/2011

Effects of an exercise programme for chronically ill and mobility-restricted elderly with structured support by the general practitioner's practice (HOMEfit) - study protocol of a randomised controlled trial

<p>Abstract</p> <p>Background</p> <p>Exercise programmes can be administered successfully as therapeutic agents to patients with a number of chronic diseases and help to improve physical functioning in older adults. Usually, such programmes target either healthy and mobile community-dwelling seniors or elderly individuals living in nursing institutions or special residences. Chronically ill or mobility-restricted individuals, however, are difficult to reach when they live in their own homes.</p> <p>A pilot study has shown good feasibility of a home-based exercise programme that is delivered to this target group through cooperation between general practitioners and exercise therapists. A logical next step involves evaluation of the effects of the programme.</p> <p>Methods/design</p> <p>The study is designed as a randomised controlled trial. We plan to recruit 210 patients (≥ 70 years) in about 15 general practices.</p> <p>The experimental intervention (duration 12 weeks)-a multidimensional home-based exercise programme-is delivered to the participant by an exercise therapist in counselling sessions at the general practitioner's practice and on the telephone. It is based on methods and strategies for facilitating behaviour change according to the Health Action Process Approach (HAPA). The control intervention-baseline physical activities-differs from the experimental intervention with regard to content of the counselling sessions as well as to content and frequency of the promoted activities.</p> <p>Primary outcome is functional lower body strength measured by the "chair-rise" test. Secondary outcomes are: physical function (battery of motor tests), physical activity (step count), health-related quality of life (SF-8), fall-related self-efficacy (FES-I), and exercise self-efficacy (SSA-Scale).</p> <p>The hypothesis that there will be differences between the two groups (experimental/control) with respect to post-interventional chair-rise time will be tested using an ANCOVA with chair-rise time at baseline, treatment group, and study centre effects as explanatory variables. Analysis of the data will be undertaken using the principle of intention-to-treat.</p> <p>Trial registration</p> <p>Current Controlled Trials <a href="http://www.controlled-trials.com/ISRCTN17727272">ISRCTN17727272</a>.</p

BlastR—fast and accurate database searches for non-coding RNAs

We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.htm

The Rab5 Effector Rabankyrin-5 Regulates and Coordinates Different Endocytic Mechanisms

The small GTPase Rab5 is a key regulator of clathrin-mediated endocytosis. On early endosomes, within a spatially restricted domain enriched in phosphatydilinositol-3-phosphate [PI(3)P], Rab5 coordinates a complex network of effectors that functionally cooperate in membrane tethering, fusion, and organelle motility. Here we discovered a novel PI(3)P-binding Rab5 effector, Rabankyrin-5, which localises to early endosomes and stimulates their fusion activity. In addition to early endosomes, however, Rabankyrin-5 localises to large vacuolar structures that correspond to macropinosomes in epithelial cells and fibroblasts. Overexpression of Rabankyrin-5 increases the number of macropinosomes and stimulates fluid-phase uptake, whereas its downregulation inhibits these processes. In polarised epithelial cells, this function is primarily restricted to the apical membrane. Rabankyrin-5 localises to large pinocytic structures underneath the apical surface of kidney proximal tubule cells, and its overexpression in polarised Madin-Darby canine kidney cells stimulates apical but not basolateral, non-clathrin-mediated pinocytosis. In demonstrating a regulatory role in endosome fusion and (macro)pinocytosis, our studies suggest that Rab5 regulates and coordinates different endocytic mechanisms through its effector Rabankyrin-5. Furthermore, its active role in apical pinocytosis in epithelial cells suggests an important function of Rabankyrin-5 in the physiology of polarised cells

New carbamate supports for the preparation of 3'-amino-modified oligonucleotides

A novel approach for the preparation of oligonucleotides carrying amino groups at the 3'-end is described. Several CPG supports having aminoalkyl groups and 3'-amino-2',3'-dideoxynucleosides linked through base-labile carbamate linkages such as 2-(2- nitrophenyl)ethoxycarbonyl and fluorenylmethoxycarbonyl were prepared using two different strategies. These supports are compatible to the standard solid phase phosphite-triester methodology and yield oligonucleotides containing amino groups at the 3'-end. Several properties of the 3'-amino oligonucleotides, such as nuclease resistance, hybridization, and preparation of oligonucleotide conjugates are discussed.Financial support from CICYT (PB92-0043) and E.E.C.C. Biomedicine and Health Programme (BMH1-CT93-1669) is gratefully acknowledged. We thank Drs P. Herdewijn, A. van Aerschot, T. Saison- Behmoaras, and W. Pfleiderer for their helpful suggestions. We are grateful to Marten Wiersma for his technical assistance.Peer reviewe

Recruiting Hard-to-Reach Subjects for Exercise Interventions: A Multi-Centre and Multi-Stage Approach Targeting General Practitioners and Their Community-Dwelling and Mobility-Limited Patients

The general practitioner (GP)’s practice appears to be an ideal venue for recruiting community-dwelling older adults with limited mobility. This study (Current Controlled Trials ISRCTN17727272) aimed at evaluating the recruiting process used for a multi-centre exercise intervention (HOMEfit). Each of six steps resulted in an absolute number of patients (N1–N6). Sex and age (for N4–N6) and reasons for dropping out were assessed. Patient database screening (N1–N3) at 15 GP practices yielded N1 = 5,990 patients aged 70 and above who had visited their GP within the past 6 months, N2 = 5,467 after exclusion of institutionalised patients, N3 = 1,545 patients eligible. Using a pre-defined limitation algorithm in order to conserve the practices’ resources resulted in N4 = 1,214 patients (80.3 ± 5.6 years, 68% female), who were then officially invited to the final assessment of eligibility at the GP’s practice. N5 = 434 patients (79.5 ± 5.4 years, 69% female) attended the practice screening (n = 13 of whom had not received an official invitation). Finally, N6 = 209 (79.8 ± 5.2 years, 74% female) were randomised after they were judged eligible and had given their written informed consent to participate in the randomised controlled trial (overall recruitment rate: 4.4%). The general strategy of utilising a GP’s practice to recruit the target group proved beneficial. The data and experiences presented here can help planners of future exercise-intervention studies