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Photoplethysmography (PPG) signals are always corrupted with motion artifacts and resulting in bad quality PPG signals. The proper designed data acquisition protocol may help in acquisition of reliable and consistence PPG signal. However, in most cases, the acquired PPG are bad quality signals. The repeated acquisition sessions sometimes can not be performed due to ethical issues and time consuming. As such an essential step is needed to deal with the corrupted PPG signal. In this report, an algorithm to select best pulse in PPG signal through comparative method of valley detection is proposed. The clinical data showed that this algorithm is a promising tool to analyze low quality PPG signals especially during data acquisition.