pFind Studio: a computational solution for mass spectrometry-based proteomics

News

2017 - 2016 -  2015 -  2014 -  2013 -  2012 -  2011 -  2010 -  2009

2017



June 22, 2017 - The pFind team is recruiting new members for 2018! For further details, please refer to the About us page.

(pFind团队招收2018年度入学学生!详情请点击About us页面。)


June 4-8, 2017 - Associate Professor Rui-Xiang Sun, Hao Chi, Dr. Chao Liu, and Wen-Feng Zeng attended the Annual Conference of American Society for Mass Spectrometry (ASMS). Dr. Chao Liu also gave an oral report about pLink2 in this conference.


May 25, 2017 - Rui-Min Wang, Zhao-Wei Wang and Xiao-Jin Zhang passed their dissertation defenses.


April 13, 2017 - Professor Shi-Sheng Sun from Northwest University visited the Institute of Computing Technology and gave a report.


March 26-29, 2017 - Dr. Wen-Feng Zeng, together with Hao Yang (a Ph.D. candidate) and Zhao-Wei Wang (a Master degree candidate), visited several collaborators in Shanghai. Wen-Feng and Hao were excited when they found a 24-year-old magnetic mass spectrometer in Prof. Hu Zhou's lab.


February 11, 2017 - The pFind team climbed Xiangshan on the Lantern Festival.


January 19, 2017 - The pFind team held its annual meeting. All pFinders summarized and reported their work in 2016.

2016



December 26, 2016 - Our paper Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications has been accepted for publication by the Journal of proteome research.


November 29, 2016 - Wen-Feng Zeng passed the dissertation defense. He studied glycoproteomics in the pFind team.


October 21, 2016 - Assistant Professor Xiaowen Liu from Indian University-Purdue University Indianapolis visited the pFind team.


September 21, 2016 - Professor David L. Tabb from Stellenbosch University visited the pFind team and gave a report.


August 19-20, 2016 - Hao Yang attended the 14th CJK Bioinformatics Training Course & Symposium.


August 10-11, 2016 - The Fourth China Workshop on Computational Proteomics successfully completed. We give thanks to all experts for their good presentations and to all participants for their support. Click here for more details.


July 9, 2016 - Dr. Chao Liu gave lectures about proteomics and data analysis for Thermo training class of proteomics and precision medicine.


June 5-9, 2016 - Dr. Hao Chi and Chao Liu attended American Society for Mass Spectrometry (ASMS) 2016.


May 27, 2016 - Hui-Jun Tu and Ji-Li Yin passed their dissertation defenses.


May 3, 2016 - Our co-authored paper pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3 has been published online in Scientific Reports.


April 15, 2016 - Associate Professor Fang-Jun Wang from Dalian Institute of Chemical Physics, CAS visited the pFind team and gave a report. Professor Meng-Qiu Dong and Professor Ping Xu attended this meeting.


March 24, 2016 - Our co-authored paper Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers has been published online in Analytical Chemistry.


February 4, 2016 - Our paper pTop 1.0: a High-accuracy and High-efficiency Search Engine for Intact Protein Identification has been accepted for publication by the Analytical Chemistry.


January 24, 2016 - The pFind team held its annual meeting. Graduated pFinders attended this meeting and shared their work experience. All pFinders summarized and reported their work in 2015.



2015



November 22, 2015 - We held a small seminar on proteogenomics. Seven experts in this field attended this seminar and gave reports. These experts were Feng Ge, Jing Li, Heng-Liang Wang, Ying-Chun Wang, Ping Xu, Gong Zhang and Li Zhu.


November 22, 2015 - Kun Zhang passed the dissertation defense.


October 17-19, 2015 - pFinders attended the 2nd CNMS. Associate Professor Rui-Xiang Sun and Dr. Chao Liu gave reports.


September 2, 2015 - Dr. Yuan Zhou from Dalian Institute of Chemical Physics, CAS visited pFind team.


August 10-12, 2015 - Lan Luo attended the 13th CJK Bioinformatics Training Course.


June 1-4, 2015 - Rui-Xiang Sun, Hao Chi, Chao Liu, and Wen-Feng Zeng attended American Society for Mass Spectrometry (ASMS) 2015


May 27, 2015 - Sheng-Bo Fan, Lan Luo, and Jian-Qiang Wu got their degrees!


May 1, 2015 - Dr. Olga Vitek reported the iPRG2015 results!

2015年4月下旬,蛋白质组信息学研究组(Proteome Informatics Research Group,iPRG)公布了由其组织的2015年蛋白质组数据分析国际评测结果。我所pFind团队提交的结果,在报告准确鉴定蛋白质数目(定性分析结果)、报告正确的含量显著差异蛋白质(定量分析结果)这两个关键指标上,表现出色。

蛋白质组信息学研究组(iPRG)前身是生物分子资源设施协会(The Association of Biomolecular Resource Facilities,ABRF)下属的生物信息学委员会(BioInformatics Committee)。其组织宗旨为评估现在生物信息应用研究水平,并对世界范围内各研究组的发展方向提供指导。为了实践该宗旨,iPRG每年最大的活动即是组织一次国际范围的蛋白质组数据分析评测。今年的评测内容是使用基于生物质谱技术的蛋白质非标记定性、定量软件,确定两个生物样品间的含量显著差异的蛋白质。评测主办方制备了两份完全相同的酵母样品,也就是说这两份样品中的蛋白质含量是一样的。这些蛋白质数目在4000到5000之间。另外,评测主办方在实验中以实验手段加入了6个含量显著差异蛋白质,做为正确答案。参评队伍要定性、定量分析数千个蛋白质,报告其中含量有显著差异的蛋白质。

今年的评测,吸引了来自世界各地共51支参评队伍,其中有10支队伍来自iPRG委员会委员领导的团队。大部分队伍提交了自己的详细信息,由此我们得知,有10支来自中国的队伍,6支来自比利时的队伍,5支来自法国的队伍,5支来自中国香港的队伍,4支来自瑞典的队伍,4支来自美国的队伍,2支来自澳大利亚的队伍,2支来自意大利的队伍,其他各队分别来自加拿大、希腊、以色列、瑞士和德国。

我所贺思敏研究员领导的pFind团队也参加了这次评测,主要工作由今年刚留所的刘超博士以及硕士二年级学生涂慧君在2015年1、2月完成。刘超博士使用pFind团队全自主开发的蛋白质定性软件pFind和蛋白质定量软件pQuant分析了本次评测的数据,并提交了结果。涂慧君使用德国马普学会Matthias Mann教授领导的实验室开发的MaxQuant软件分析了本次评测的数据,并提交了结果。其他有多支队伍也使用MaxQuant软件或自己开发的以及各主流商业软件分析本次评测的数据,并提交结果。

2015年4月下旬,美国普渡大学Olga Vitek博士公开报告了此次评测结果(http://www.abrf.org/index.cfm/group.show/ProteomicsInformaticsResearchGroup.53.htm)。我所pFind团队刘超博士提交的结果,报告准确鉴定蛋白质数目为4284个。pFind团队涂慧君提交的结果,报告准确鉴定蛋白质数目为3851个。其他队伍报告的准确鉴定蛋白质数目从3800左右向下到1500左右不等。

本次评测最核心的任务是报告样品间正确的含量显著差异蛋白质。我所pFind团队刘超博士提交的结果,精确报告了6个正确答案蛋白质,没有多报告一个假阳,没有遗漏一个真阳。涂慧君提交的结果,报告了7个蛋白质,其中包含了6个正确答案,多报告了1个假阳。另有一支队伍也准确报告了6个正确答案。其他各队稍好的与涂慧君结果相当,或者没有报告错误蛋白质,但遗漏正确蛋白质。最差的队伍遗漏3个,错报了近250个蛋白质。


April. 8, 2015 - Dr. Bernard Delanghe, Dr. Yue Xuan and other friends from Thermo Fisher visit pFinders. Dr. Bernard Delanghe is the product manager of proteomics software of Thermo Fisher.


Feb. 6, 2015 - pFind Team is the outstanding team of ICT!



2014



Dec. 15, 2014 - Dr. Zuo-Fei Yuan returns home. He got Ph.D. degree in June, 2012. Now he works as a postdoctor at University of Pennsylvania.


Nov. 12-13, 2014 - The Third China Workshop on Computational Proteomics successfully completed. We give thanks to all experts for their good presentations and to all participants for their support. Click here for more details.


June 17-21, 2014 - Kun Zhang attended Korea-Japan-China Bioinformatics Training Course. He gave a report titled "Identifying novel genes and gene refinements in Thermoanaerobacter tengcongensis".


May 19, 2014 - CNCP.ict.ac.cn is online now.

第三届中国计算蛋白质组学研讨会将于2014年11月12日、13日在中科院计算所举行。
截止2014年5月15日,CNCP-2014组委会已经邀请到如下10位学者作大会报告(汉语拼音字母序):
丁琛 葛英 林诚 刘晓文 汤海旭 王春光 王恒樑 应万涛 钟鸿英 周虎
欢迎海内外专家学者莅临指导!
访问CNCP2014获取更多关于中国计算蛋白质组学研讨会的信息!

Apr. 25, 2014 - The friends from Dalian Institute of Chemical Physics, Chinese Academy of Sciences visited pFinders.


Apr. 23, 2014 - 计算蛋白质组学领域知名学者、美国密西根大学副教授Alexey I. Nesvizhskii博士访问pFinder,并做精彩报告。




2013



Dec. 17, 2013 - 2013计算所生物信息组学术交流会在计算所四层召开。会议由迟浩博士主持,韩仁敏、张静蓉、张昆、邬龙、罗海涛、卜德超、张海仓和许情8位同学做了精彩的报告,贺思敏、卜东波、孙瑞祥、张法、赵屹五位老师以及生物信息组的全体同学参加。大家从选题新颖性、方法创新性、表述清晰程度、以及实验效果四个方面对报告进行了评比,最终张静蓉同学的报告《Iterative methods in large field electron microscope tomography and its parallelization》获得最高的分数。

计算所生物信息组学术交流会每年举办一次,旨在增进各研究组间的学术交流,鼓励青年人勇于创新、积极拼搏、善于表达。会上各位老师、同学给报告人提出了很多有意义的建议,会后大家进行了热烈的讨论。该交流会得到了大家的一致好评,达到了预期效果。

图 张静蓉同学介绍CT成像技术


Dec. 1, 2013 - Kun He and Long Wu get their Master Degrees!


Sep. 7, 2013 - The 8th CNHUPO Annual Congress successfully completed. Teacher Sun and ChiHao made reports in this congress and we learned a lot. Click here for more details.


Apr. 8, 2013 - Dr. Bandeira and Jeong of UCSD visited pFinders.



2012



Nov. 16, 2012 - The Second China Workshop on Computational Proteomics successfully completed. We give thanks to all experts for their good presentations and to all participants for their support. Click here for more details.


Sep. 1, 2012 - The Tenth Uppsala Conference on Electron Capture and Transfer Dissociation is online.

This international conference is co-organized by the Institute of Computing Technology (ICT), Chinese Academy of Sciences and National Institute of Biological Sciences (NIBS),China, which will be held in Beijing Friendship Hotel during Feb.17 to 21, 2013.
Click http://uppcon2013.csp.escience.cn/ for details.


Aug. 29, 2012 - CNCP.ict.ac.cn is online now.

第二届中国计算蛋白质组学研讨会将于2012年11月14日、15日在中科院计算所举行。
本次会议的特邀专家有(汉语拼音字母序):
邓海腾 关慎恒 何增有 胡良海 蒋太交 赖仞 李婧 林熙宁 马斌 苗龙 宁康 谭敏佳 田志新
王柏臣 王立顺 薛宇 杨兵 杨胜勇 张弓 张扬 张红雨 张纪阳 张京芬 章冰 赵雁林
欢迎海内外专家学者莅临指导!
访问CNCP2010获取更多关于第一届中国计算蛋白质组学研讨会的信息!

July 9, 2012 - The paper Identification of cross-linked peptides from complex samples has been published online in Nature Methods.

        2012年7月8日,北京生命科学研究所董梦秋实验室与中科院计算技术研究所贺思敏教授领导的pFind研究团队合作在《Nautre Methods》在线发表题为“Identification of Cross-linked Peptides from Complex Samples”的文章。
  
        蛋白质化学交联结合质谱鉴定技术(chemical cross-linking of proteins coupled with mass spectrometry analysis,CXMS)能够提供丰富的蛋白质折叠与蛋白质相互作用的信息。该技术能够帮助测定蛋白质的结构以及蛋白质复合物亚基之间相互作用的界面。
  
        CXMS技术虽然只能提供鉴定到的交联氨基酸之间的空间距离信息,但不需要蛋白质晶体,也不需要大量的高度纯化的蛋白,是对现有的结构生物学技术的补充。CXMS还有望与蛋白质免疫共沉淀或pull-down 结合,辨识直接相互作用的蛋白。CXMS对蛋白样品的量与纯度要求较低,实验周期短,具备广泛的适用性。
  
        在这篇论文中,研究人员报告了一套完整的基于高精度质谱鉴定化学交联肽段的方法。他们优化了CXMS的各个实验环节,并与中科院计算所合作开发了化学交联多肽的鉴定软件pLink。
  
        pLink可以处理复杂样品如全细胞裂解液的CXMS数据,能够有效估算交联多肽鉴定的假阳性率,并且对谱图进行自动标注。研究人员用体外纯化的简单蛋白质样品、大的蛋白质复合物、免疫共沉淀样品、以及大肠杆菌和秀丽线虫全细胞裂解液,充分证明了CXMS和pLink软件的有效性。

Jun. 27, 2012 - Dr. Zhi-Xin Tian of DICP visited pFinders.


Jun. 4, 2012 - Zuo-Fei Yuan gets his doctoral degree.

His Ph.D. dissertation is "Peptide Identification Based on Large-scale Mass Spectra". Congratulations!
袁作飞的博士毕业论文题目为《基于规模化质谱数据的肽鉴定方法研究》。他毕业后将去美国宾夕法尼亚大学做博士后。恭喜袁作飞!
照片左起:陈熙霖、黄铁军、贺思敏、袁作飞、董梦秋、黄庆明、山世光


Mar. 26, 2012 - The paper Nematode sperm maturation triggered by protease involves sperm-secreted serine protease inhibitor (Serpin) has been published in PNAS.

        2012年1月17日,《美国国家科学院院刊》(Proceedings of the National Academy of Sciences, PNAS)在线发表了中国科学院生物物理研究所苗龙课题组和北京生命科学研究所董梦秋课题组合作的最新研究成果:Nematode sperm maturation triggered by protease involves sperm-secreted serine protease inhibitor (Serpin)。该研究在Ascaris suum线虫中鉴定了两个精子激活调控相关的蛋白因子:丝氨酸蛋白酶抑制因子As_SRP-1和类胰蛋白酶As_TRY-5;阐述了它们之间相互协同作用调控精子成熟的机理,为精子竞争研究提供了全新的分子机制。
        广泛发生的寄生虫病对人类健康和农牧业生产具有长期潜在甚至灾难性的影响。仅蛔虫而言,目前全球约有12亿人感染。蛔虫感染可导致儿童营养匮乏、体质受损、认知发育缺陷甚至死亡;蛔虫感染造成养殖业巨大的经济损失。因此,研究蛔虫精子发育和受精机理无疑对于控制其传播具有重要的指导意义;同时,猪蛔虫(Ascaris suum)精子细胞是研究阿米巴细胞运动极好的模式材料,了解其运动机制可进一步揭示阿米巴细胞运动的调控模式。完成减数分裂的精子细胞需要一个成熟的过程(即精子获能或精子活化)才能发育为功能性精子。目前,关于这一过程所涉及的生理、生化及精子形态改变的机理还了解甚少。
        在该研究中,作者通过多种实验手段,发现猪蛔虫精子细胞在活化过程中通过调节性胞吐释放出一个丝氨酸蛋白酶的抑制因子(As_SRP-1)。进一步研究发现,该蛋白被释放后执行了两种功能:(1)As_SRP-1结合到已经活化或开始活化的精子表面,维持伪足细胞骨架的动态组装;As_SRP-1的结合被破坏,精子的运动能力即随之丧失。(2)As_SRP-1抑制一个由输精管末端分泌的、诱导精子活化的丝氨酸蛋白酶As_TRY-5。通过抑制As_TRY-5的活性,As_SRP-1阻碍了周围其它精子细胞的活化。胞吐释放的丝氨酸蛋白酶抑制因子的“双刃剑”功能一方面在雄性体内抑制其它精子的提前活化,这种精子间的互助合作极大地保证了雄性个体在交配时精子的成功转移;另一方面,交配完成后在雌性生殖道内,这种精致的负反馈调节驱动精子竞争从而实现受精的最优化选择。
        在动物行为和社会生物学方面,精子竞争、性别冲突与进化是一个研究热点。精子竞争是塑造进化过程的选择性力量。传统研究认为,运动活跃的精子细胞只是被动地参与由多种体细胞分泌蛋白组成的精液所介导的精子竞争。该研究发现,精子细胞在活化的过程中主动分泌蛋白从而影响自身和其它精子细胞的成熟,为宏观上广泛存在的精子竞争提供了全新的分子机制。另外,其它动物如昆虫、小鼠的精液里也有蛋白酶和蛋白酶抑制剂,所以类似的调节机制可能广泛存在。
        这篇文章的另一个亮点是不依赖于蛋白数据库的肽段从头测序(de novo sequencing)。以前的从头测序效果欠佳,鲜有实际应用。为了此项研究的需要,北京生命科学研究所董梦秋研究组与中国科学院计算所贺思敏研究组共同开发了肽段从头测序的质谱实验流程和算法,达到了与数据库搜索相当的鉴定效果。本文中的两个蛋白As_SRP-1和As_TRY-5都是用肽段从头测序技术pNovo鉴定到的,表明pNovo足以支持生物学研究,尤其是对于新蛋白(序列未被收纳到现有数据库中)的鉴定有极大的帮助。最新公布的猪蛔虫基因组草图[Nature 479, 529–533 (24 November 2011)]将极大地推进后续研究的进行。
        生物物理研究所赵艳梅博士是本文第一作者。苗龙研究员和北京生命科学研究所董梦秋研究员是本文共同通讯作者。该研究得到科技部国家重点基础研究973计划、国家自然科学基金委员会、中国科学院“百人计划”和北京市政府的资助。本研究在样品制备方面得到了山东省新程金锣肉制品集团有限公司的无偿援助。
        (中科院生物物理所供稿)


2011



Nov. 3, 2011 - Our paper pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra has been accepted for publication by the journal Proteomics.


Jun. 9, 2011 (Munich, Germany) - Zuo-Fei Yuan attended MaxQuant Summer School 2012.



2010



Dec. 13, 2010 (Dalian, China) - pFinders visited Dr. Li-Hua Zhang and Zhen Liang of DICP.


Nov. 30, 2010 - Dr. Marshall Bernteam visited pFinders.


Nov. 12, 2010 - The First China Workshop on Computational Proteomics successfully completed. We give thanks to all experts for their good presentations and to all participants for their support. Click here for more details.


Oct. 19, 2010 - Dr. Daniel Figeys and Hu-Zhou visited pFinders.


Oct. 11, 2010 - Dr. Peipei Ping visited pFinders.


Aug. 26, 2010 - Dr. Ting Chen visited pFinders.


May. 3, 2010 - Dr. Shengheng Guan visited pFinders and Dong Lab of NIBS.


Apr, 2010 (Shanghai, China) - pFinders visited Dr. Rong Zeng of SIBS.


Jan, 2010 - pFinders visited Dr. Si-Qi Liu of DICP.



2009 and before



Oct. 23, 2009 (Dalian, China) - pFinders visited Dr. Li-Hua Zhang and Zhen Liang of DICP.


Oct. 15, 2008 - John Yates visited pFinders and Dong Lab.