恐龙、pFind和商业

  科学家从6800万年前的暴龙化石中成功鉴定出了胶原蛋白,蛋白分析结果也进一步佐证了鸟类起源于恐龙的进化理论。论文发表在2007年4月13日出版的Science(VOL 316 SCIENCE 280-285)上。鉴定这些胶原蛋白用的是离子阱串联质谱技术,软件是SEQUEST。文章后面说:

  “The fact that sequenceable collagen was very abundant in the mastodon sample, which could be approximately half a million years old, also sheds light on the fact that sequenceable protein lasts much longer than 1 million years.”

  还提到,即使没有基因组序列,质谱技术和生物信息学也可以有所作为:

  “As technologies become more refined and protein extraction techniques are optimized, more informative material may be recovered. This holds promise for future work on other fossil material showing similar preservation, but also demonstrates a method for obtaining protein sequences from rare or endangered extant organisms whose genomes have note been sequenced. The MS- and bioinformatics-based approach we have used can be applied not only to obtain sequences from extinct organisms, but also to obtain protein sequences from extant organisms whose genomes have not been sequenced and to discover mutations in diseased tissues such as cancers.”

  希望有一天,生物学家在Science、Nature或Cell上发表这种有趣的牛文章时能提到pFind的名字。

  明天去北京蛋白质组研究中心。最近连续去合作单位,请生物学家试用。用户认为pFind有望超过SEQUEST。至于Mascot,其实算法也可以比,但工程细节上差距不小。我们的现实问题是科研人员精力有限,软件开发效率不高,团队无法做到快速反馈迭代。

  昨天写email:要保证软件开发质量,就需要职业软件工程师,就需要钱。pFind想更进一步,尤其是着眼海外市场的话,必须按游戏规则来玩,我们得考虑用商业机制来推动了。

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