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BackgroundQuantitative proteomics technologies have been developed to comprehensively identify and quantify proteins in two or more complex samples. Quantitative proteomics based on differential stable isotope labeling is one of the proteomics quantification technologies. Mass spectrometric data generated for peptide quantification are often noisy, and peak detection and definition require various smoothing filters to remove noise in order to achieve accurate peptide quantification. Many traditional smoothing filters, such as the moving average filter, Savitzky-Golay filter and Gaussian filter, have been used to reduce noise in MS peaks. However, limitations of these filtering approaches often result in inaccurate peptide quantification. Here we present the WaveletQuant program, based on wavelet theory, for better or alternative MS-based proteomic quantification.ResultsWe developed a novel discrete wavelet transform (DWT) and a 'Spatial Adaptive Algorithm' to remove noise and to identify true peaks. We programmed and compiled WaveletQuant using Visual C++ 2005 Express Edition. We then incorporated the WaveletQuant program in the Trans-Proteomic Pipeline (TPP), a commonly used open source proteomics analysis pipeline.ConclusionsWe showed that WaveletQuant was able to quantify more proteins and to quantify them more accurately than the ASAPRatio, a program that performs quantification in the TPP pipeline, first using known mixed ratios of yeast extracts and then using a data set from ovarian cancer cell lysates. The program and its documentation can be downloaded from our website at http://systemsbiozju.org/data/WaveletQuant.

In this paper, a reliable scheme based on star topology is proposed by introducing group protection. Depending on interconnecting fibers, all optical network units (ONUs) are divided into some groups and each group contains 2 ONUs.Through these groups, the network can not only realize efficient transmission of local area network service between adjacent ONUs but also provide mutual protection for ONUs in a group when distribution fibers happen to faults. By using the backup pathway, the network can further provide protections for feeder fibers when they fall in faults. With the help of the optical tunable receiver in ONU, dynamic bandwidth allocation algorithm is also supported to realize flexible bandwidth allocation in 1 group. By the subtly design, the network can realize passivity (there are no active devices in remote nodes), modularization, and scalability. By utilizing amplitude modulation, differential phase shift keying modulation and reflective semiconductor optical amplifier technology, wavelength triple reuse is also achieved. Finally, the results of simulation and performance analysis demonstrate the feasibility of the architecture.KEYWORDS group protection, high reliability, LAN, metro-access network, modularization | INTRODUCTIONWith the rapid development of real-time services, such as teleconference, telemedicine, and online education, the more efficient way of communication needs to be considered, especially for the future optical network. 1 However, direct communication among optical network units (ONUs) is not supported in the traditional optical networks. The communication information needs to be firstly transmitted to the optical line terminal (OLT) and then transmitted to the destination ONUs. This will cause some problems, for example, raising the burden of OLT and even resulting in the information congestions, taking up the bandwidth of up and downstream signals, increasing transmission delay, and so on. To solve these problems, the solutions supporting direct communications among ONUs have been proposed. 2 Meanwhile, optical metro-access network can integrate traditional metro and access layers into metro-access layer, which will meet the flattening development trend of future optical network. 3 In a short, it is becoming increasingly important to support direct communication among ONUs for metro-access network.In the support of services, the schemes supporting local area network (LAN) service can be classified into 5 categories in general: additional transceiver, utilizing upstream signals, broadcasting, virtual ring, and ONU ring. Garg et al transmit and receive LAN service together with downstream and upstream services by placing a transceiver in OLT or remote node (RN). 4 The LAN signals will be transmitted to OLT or RN from initiative ONU and next to destination ONU. Wu et al transmit LAN service through orthogonal modulation technology. 5 By utilizing the light source of upstream signals, the LAN signals are produced. Garg et al broadcast the LAN signals to all output ports of a 8 ×...