Whenever human beings interact with each other, they exchange or express opinions, emotions and sentiments. These opinions can be expressed in text, speech or images. Analysis of these sentiments is one of the popular research areas of present day researchers. Sentiment analysis, also known as opinion mining tries to identify or classify these sentiments or opinions into two broad categoriespositive and negative. Much work on sentiment analysis has been done on social media conversations, blog posts, newspaper articles and various narrative texts. However, when it came to identifying emotions from scientific papers, researchers used to face difficulties due to the implicit and hidden natures of opinions or emotions. As the citation instances are considered inherently positive in emotion, popular ranking and indexing paradigms often neglect the opinion present while citing. Therefore in the present paper, we deployed a system of citation sentiment analysis to achieve three major objectives. First, we identified sentiments in the citation text and assigned a score to each of the instances. We have used a supervised classifier for this purpose. Secondly, we have proposed a new index (we shall refer to it hereafter as M-index) which takes into account both the quantitative and qualitative factors while scoring a paper. Finally, we developed a ranking of research papers based on the M-index. We have also shown the impacts of M-index on the ranking of scientific papers.