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A meta-analysis of the effect of a mono-component bacterial protease (RONOZYME® ProAct) on the apparent ileal digestibility of amino acids in poultry and swine diets was conducted to examine functional patterns, mean effects and variability of response. A total of 25 independently-conducted experiments were included comprising a total of 804 datapoints. The mean response to protease was +3.74% (SE 1.1%, P<0.001) and this ranged from +5.6% for Thr (SE 1.2%, P<0.001) to +2.7% for Glu (SE 1.2%, P<0.05). For the most economically critical amino acids (Lys, Cys, Met and Thr) the mean response was 4.5%. The effect of protease was independent of geography, animal species and diet composition (P>0.05). However, the inherent digestibility of amino acids in the control diet as a single explanatory term explained around 47% of the variance (P<0.001) in effect. When the inherent digestibility of amino acids in the control diet was less than 70% protease addition improved amino acid digestibility in 90% of cases with a mean improvement of around 10%. When the inherent digestibility of amino acids in the control diet was more than 90% there was a protease-mediated improvement in digestibility in only 60% of cases with a mean improvement of around 2%. It can be concluded that the inherent digestibility of amino acids in the diet without protease supplementation is the primary explanatory term for the efficacy of this exogenous protease, demonstrating that it is highly effective in improving the digestibility of amino acids across a wide range of feed ingredients. Benchmarking diets or feed ingredients as to their relative nutritional value would enhance the ability of nutritionists to determine the likely return on investment on use of bacterial proteases in their operation

Motivation: Tandem mass spectrometry allows for high-throughput identification of complex protein samples. Searching tandem mass spectra against sequence databases is the main analysis method nowadays. Since many peptide variations are possible, including them in the search space seems only logical. However, the search space usually grows exponentially with the number of independent variations and may therefore overwhelm computational resources. Results: We provide fast, cache-efficient search algorithms to screen large peptide search spaces including non-tryptic peptides, whole genomes, dozens of posttranslational modifications, unannotated point mutations and even unannotated splice sites. All these search spaces can be screened simultaneously. By optimizing the cache usage, we achieve a calculation speed that closely approaches the limits of the hardware. At the same time, we control the size of the overall search space by limiting the combinations of variations that can co-occur on the same peptide. Using a hypergeometric scoring scheme, we applied these algorithms to a dataset of 1 420 632 spectra. We were able to identify a considerable number of peptide variations within a modest amount of computing time on standard desktop computers. Availability: PepSplice is available as a C++ application for Linux, Windows and OSX at www.ti.inf.ethz.ch/pw/software/pepsplice/. It is open source under the revised BSD license. Contact: franz.roos@alumni.ethz.ch or jacob@in.tum.de Supplementary information: Supplementary data are available at Bioinformatics online

An efficient and robust method to measure vitamin D (25-hydroxy vitamin D3 (25(OH)D3) and 25-hydroxy vitamin D2 in dried blood spots (DBS) has been developed and applied in the pan-European multi-centre, internet-based, personalised nutrition intervention study Food4Me. The method includes calibration with blood containing endogenous 25(OH)D3, spotted as DBS and corrected for haematocrit content. The methodology was validated following international standards. The performance characteristics did not reach those of the current gold standard liquid chromatography-MS/MS in plasma for all parameters, but were found to be very suitable for status-level determination under field conditions. DBS sample quality was very high, and 3778 measurements of 25(OH)D3 were obtained from 1465 participants. The study centre and the season within the study centre were very good predictors of 25(OH)D3 levels (P<0·001 for each case). Seasonal effects were modelled by fitting a sine function with a minimum 25(OH)D3 level on 20 January and a maximum on 21 July. The seasonal amplitude varied from centre to centre. The largest difference between winter and summer levels was found in Germany and the smallest in Poland. The model was cross-validated to determine the consistency of the predictions and the performance of the DBS method. The Pearson's correlation between the measured values and the predicted values was r 0·65, and the sd of their differences was 21·2 nmol/l. This includes the analytical variation and the biological variation within subjects. Overall, DBS obtained by unsupervised sampling of the participants at home was a viable methodology for obtaining vitamin D status information in a large nutritional study.

A meta-analysis of the effect of a mono-component bacterial protease (RONOZYME® ProAct) on the apparent ileal digestibility of amino acids in poultry and swine diets was conducted to examine functional patterns, mean effects and variability of response. A total of 25 independently-conducted experiments were included comprising a total of 804 datapoints. The mean response to protease was +3.74% (SE 1.1%, P<0.001) and this ranged from +5.6% for Thr (SE 1.2%, P<0.001) to +2.7% for Glu (SE 1.2%, P<0.05). For the most economically critical amino acids (Lys, Cys, Met and Thr) the mean response was 4.5%. The effect of protease was independent of geography, animal species and diet composition (P>0.05). However, the inherent digestibility of amino acids in the control diet as a single explanatory term explained around 47% of the variance (P<0.001) in effect. When the inherent digestibility of amino acids in the control diet was less than 70% protease addition improved amino acid digestibility in 90% of cases with a mean improvement of around 10%. When the inherent digestibility of amino acids in the control diet was more than 90% there was a protease-mediated improvement in digestibility in only 60% of cases with a mean improvement of around 2%. It can be concluded that the inherent digestibility of amino acids in the diet without protease supplementation is the primary explanatory term for the efficacy of this exogenous protease, demonstrating that it is highly effective in improving the digestibility of amino acids across a wide range of feed ingredients. Benchmarking diets or feed ingredients as to their relative nutritional value would enhance the ability of nutritionists to determine the likely return on investment on use of bacterial proteases in their operation

Motivation: Tandem mass spectrometry allows for high-throughput identification of complex protein samples. Searching tandem mass spectra against sequence databases is the main analysis method nowadays. Since many peptide variations are possible, including them in the search space seems only logical. However, the search space usually grows exponentially with the number of independent variations and may therefore overwhelm computational resources. Results: We provide fast, cache-efficient search algorithms to screen large peptide search spaces including non-tryptic peptides, whole genomes, dozens of posttranslational modifications, unannotated point mutations and even unannotated splice sites. All these search spaces can be screened simultaneously. By optimizing the cache usage, we achieve a calculation speed that closely approaches the limits of the hardware. At the same time, we control the size of the overall search space by limiting the combinations of variations that can co-occur on the same peptide. Using a hypergeometric scoring scheme, we applied these algorithms to a dataset of 1 420 632 spectra. We were able to identify a considerable number of peptide variations within a modest amount of computing time on standard desktop computers. Availability: PepSplice is available as a C++ application for Linux, Windows and OSX at www.ti.inf.ethz.ch/pw/software/pepsplice/. It is open source under the revised BSD license. Contact: franz.roos@alumni.ethz.ch or jacob@in.tum.de Supplementary information: Supplementary data are available at Bioinformatics online