ChimST: An Efficient Spectral Library Search Tool for Peptide Identification from Chimeric Spectra in Data-Dependent Acquisition.

Accurate and sensitive identification of peptides from MS/MS spectra is a very challenging problem in computational shotgun proteomics. To tackle this problem, spectral library search has been one of the competitive solutions. However, most existing library search tools were developed on the basis of one peptide per spectrum, which prevents them from working properly on chimeric spectra where two or more peptides are co-fragmented. In this work, we present a new library search tool called ChimST, which is particularly capable of reliably identifying multiple peptides from a chimeric spectrum. It starts with associating each query MS/MS spectrum with MS precursor features. For each precursor feature, there is a list of peptide candidates extracted from an input spectral library. Then, it takes one peptide candidate from each associated feature and scores how well they could collectively interpret the query spectrum. The highest-scoring set of peptide candidates are finally reported as the identification of the query spectrum. Our experimental tests show that ChimST could significantly outperform the three state-of-the-art library search tools, SpectraST, reSpect, and MSPLIT, in terms of the numbers of both peptide-spectrum matches and unique peptides, especially when the acquisition isolation window is broad.

A Hardware Pseudo-Random Number Generator Using Stochastic Computing and Logistic Map.

Recent research showed that the chaotic maps are considered as alternative methods for generating pseudo-random numbers, and various approaches have been proposed for the corresponding hardware implementations. In this work, an efficient hardware pseudo-random number generator (PRNG) is proposed, where the one-dimensional logistic map is optimised by using the perturbation operation which effectively reduces the degradation of digital chaos. By employing stochastic computing, a hardware PRNG is designed with relatively low hardware utilisation. The proposed hardware PRNG is implemented by using a Field Programmable Gate Array device. Results show that the chaotic map achieves good security performance by using the perturbation operations and the generated pseudo-random numbers pass the TestU01 test and the NIST SP 800-22 test. Most importantly, it also saves 89% of hardware resources compared to conventional approaches.