News in the lab

  • Welcome to new post-doctoral fellow Felipe Leprevost. Felipe joins us from the Oswaldo Cruz Foundation (known as Fiocruz) in Curitiba, Brazil. Felipe received his Ph.D. in Bioinformatics and Computational Biology.

  • Congratulations to Andy Kong and Dattatreya Mellacheruvu, who received travel awards to attend the US HUPO Conference in Tempe Arizona. Andy presented his work on GPU accelerated MS/MS database search, and Datta presented an update on our CRAPome resource for the analysis of protein-protein interaction data. At the same conference Chih-Chiang Tsou presented an update on his DIA-Umpire tool for SWATH/DIA mass spectrometry data, Alexey taught a short course on protein interactions (with Ileana Cristea) and presented on the subject of false discovery rates in large proteomics and proteogenomics datasets in an evening Characterizing Confidence in Complete Proteome Experiments.

  • Congratulations to Chih-Chiang Tsou who was selected to receive a 2015 Graduate Student Award from the American Society for Mass Spectrometry (ASMS)! The ASMS Graduate Student Award recognizes graduate students whose academic achievements and current mass spectrometry research display a high level of excellence and distinction. The award will be presented during the ASMS business meeting on Wednesday, June 3, 2015.

  • "DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics" has been published in Nature Methods. You can find links to this and all other computational tools on our SOFTWARE page.

  • Congratulations to Dattatreya Mellacheruvu who successfully defended his Ph.D. thesis "A computational and informatics framework for the analysis of affinity purification mass spectrometry data and reconstruction of protein interaction network"!

  • LuciPHOr2, computational tool for localizing sites of post-tanslation modifications, is published in Bioinformatics. You can find links to this and all other tools on our SOFTWARE page.

  • Congratulations to Avinash Shanmugam, Ph.D student in the lab, who received a poster award for his presentation on "Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS" at the 3rd Mass Spectrometry Special Interest Group (MS-SIG) workshop during the 2014 ISMB meeting in Boston, MA. The manuscript has now been published in the Journal of Proteome Research.

  • Congratulations to Dattatreya Mellacheruvu, Ph.D student in the lab, who received the 2014 Endowment for the Development of Graduate Education (EDGE) award from the University of Michigan.

  • Congratulations to Andy Kong, Ph.D. student in the lab, who received the Pre-doctororal Fellowship Award from the Natural Sciences and Engineering Research Council of Canada (NSERC).

  • CRAPome resource has been published in Nature Methods. The Contaminant repository for affinity purification (CRAPome) is a database of annotated negative controls contributed by the proteomics research community. For more details visit the Crapome website.

  • Congratulations to Scott Walmsley, who received a Young Investigator Travel Award to attend the Mass Spectrometry: Applications to the Clinical Lab (MSACL) Conference in San Diego in February 2013. Scott will present his collaborative work with the National Institute of Standards and TEchnology (NIST) on the analysis of trypsin digestion in proteomics.

  • Congratulations to Alejandro Balbin, whose poster on "Reconstructing targetable pathways in lung cancer by integrating transcriptome, proteome and phosphoproteome" received a special recognition (scored in the top 2.5% of abstracts presented in the poster sessions) at the 2012 American Association for Cancer Research meeting in Chicago, IL.

  • Special issue of the journal Proteomics on Protein Complexes and Interaction Networks is now published. The special issue was Co-Edited by Alexey Nesvizhskii and Anne-Claude Gingras, and you can find the Editorial introducing the special issue here. The special issue contains 18 comprehensive review articles from the leading labs. We sincerely thank all the authors (and also the reviewers) whose contribution made this special issue outstanding. The manuscripts cover a wide area of experimental and computational topics, including a historical perspective, non-mass spectrometry-based approaches, structural view of protein interactions and complexes, affinity purification mass spectrometry, and computational analysis.

  • Read a new comprehensive review:
    Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments.
    Nesvizhskii AI.
    Proteomics. 2012 12:1639-55

  • 2012 ISMB Conference, Mass Spectrometry Special Interest Group (MS-SIG) meeting
    July 14, 2012, Long Beach, California
    This is the first time there is a computational proteomics SIG meeting at ISMB. The special emphasis will be on label vs. label-free protein quantification, and on proteomics applications in biology and medicine.

  • SAINT-MS1 method and software for scoring label-fee intensity based AP-MS protein interaction data is published in Journal of Proteome Research. For more details see SOFTWARE page, and visit the SAINT website at

  • 2012 Great Lakes Bioinformatics Conference
    May 13-16, 2012, Ann Arbor, Michigan
    A special session co-organized by Rob Ewing and Alexey Nesvizhskii on "Computational Proteomics: Understanding Network Perturbations in Cancer" took place on Wednesday, May 15. We had excellent presentations and great attendence. The speakers were Rob Ewing and Mehmet Koyuturk (Case Western) and one of our trainees, Alejandro Balbin (Ph.D. student, Bioinformatics, University of Michigan).

  • Congratulations to Kang Ning, whose article "Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data", published in Journal of Proteome Research (2012) 11:2261-71, was among the most read articles in that journal in the month of April 2012.

  • Alexey Nesvizhskii has accepted the position of Section Editor in the area of Proteomics for the leading bioinformatics open access journal BMC Bioinformatics.

  • Our article , a Guided Tour of the Trans-Proteomic Pipeline, published in Proteomics, is the most cited article among papers published in the journal in 2010 and 2011.

  • Our manuscript describing new computational approach and software tool iProphet is published in the journal Molecular and Cellular Proteomics. iProphet is an important addition to the widely used Trans-Proteomic Pipeline (TPP) suite of tools which include PeptideProphet and ProteinProphet. It significantly improves the accuracy and sensitivity of shotgun proteomic data analysis and allows integration of multiple database search engines. See SOFTWARE page for more details. Access the publication at Molecular and Cellular Proteomics and download the entire TPP software suite here.

  • We have published our tool for extracting adjusted spectral counts in the journal Proteomics. Abacus is an open source JAVA program that runs on all major OS platforms. Abacus generates a spreadsheet listing the proteins present in multiple TPP results along with the protein's peptide and spectral counts. For more details see SOFTWARE and also visit the Abacus website at

  • Congratulations to Scott Walmsley, who received a travel award to attend the US HUPO Conference in San Francisco. Scott will present his collaborative work with the National Institute of Standards and Technology (NIST) on the analysis of reproducibility and specificity of trypsin digestion in proteomics.

  • Nesvizhskii and Gingras labs publish in Nature Methods the new version of the statistical tool SAINT for scoring protein interaction data generated using affinity purification-mass spectrometry (AP-MS). Access the publication at Nature Methods and download the free software SAINT 2.0 at

  • Congratulations to Alejandro Balbin (Ph.D. student, Bioinformatics) who was awarded F31 Ruth L. Kirschstein National Research Service Awards for Individual Predoctoral Fellowships to work on the project "Reconstructing targetable pathways in lung cancer using a bioinformatics approach".

  • RECOMB Satellite Conference on Computational Proteomics 2011
    March 11-13, 2011 San Diego CA
    The goal of this meeting is to bring together computational and experimental scientists in the area of computational proteomics and mass spectrometry to discuss current research directions and latest findings, as well as to establish new collaborations to meet the algorithmic and statistical challenges in high-throughput proteomics.
    Co-Chairs of the Program Committee: Alexey Nesvizhskii and Nuno Bandeira (UC San Diego)
    Key Dates:
    * Paper submissions begin: November 1, 2010
    * Paper submissions deadline: December 1, 2010
    * Paper decisions announced: January 15, 2011

  • Read a new comprehensive review:
    A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.
    Nesvizhskii AI.
    J Proteomics. 2010 73:2092-123

  • "A global protein kinase and phosphatase interaction network in yeast" has been published in Science (Breitkreutz et al. Science 328, 1043 - 104 (2010)). The Tyers, Nesvizhskii and Gingras labs team up to provide a comprehensive interaction map for yeast kinases and phosphatases. See high-confidence interactions deposited in the BioGrid and IntAct databases, the dedicated website, access raw data at Tranche, and download our software SAINT.

  • Our manuscript describing the statistical model for peptide identification in shotgun proteomics, which introduced the concept of local and global FDR in proteomics, has reached 1000 citation mark according to Google Scholar.

  • New Proteome Informatics of Cancer Training Program (T32 grant) at The University of Michigan has been funded by the NCI (Director: Phil Andrews, Associate Director: Alexey Nesvizhskii). More info and how to apply.

  • Alexey Nesvizhskii has been named the Senior Editor of both Proteomics and Proteomics-Clinical Applications in the area of Bioinformatics and Biostatistics. These are the two leading journals in the field, published by Wiley-VCH. See the announcement here.

  • Course Announcement, Winter 2011 semester. A 3 credit course on proteomics and its biomedical applications. Proteomics and Informatics, Bioinf 551/ Chem 551/ BiolChem 551/ Path 551/ BioMedEng 551, meeting Tuesdays, Thursdays 1:00 - 2:30 PM. See here for more information.

The lab in the News

  • DIA-Umpire computational workflow published in Nature Methods was discussed in GenomeWeb (January 2015)

  • Alexey Nesvizhskii was interviewed by GenomeWeb (November 2014) on the subject of proteogenomics following the publication of his comprehensive review on proteogenomics in Nature Methods

  • Congratulations to our friend and long-term collaborator Anne-Claude Gingras (Samuel Lunenfeld Research Institute, Toronto) who was profiled in ASMBM Today. Read here (August 2011) about her view on the role of SAINT and other computational tools co-developed by Gingras and Nesvizhskii labs in proteomics research.

  • Press-release about our computational method SAINT for AP-MS data by our collaborators at Samuel Lunenfeld Research Institute (December 8, 2010)

  • Our recent work on the development of computational methods for AP-MS protein interaction data is mentioned in ``Protein-Protein Interaction Technologies Toward a Human Interactome`` (Science, 2010)

  • Read about Dr. Nesvizhskii and the research in the lab in e-Protein Newsletter (issue 6, 2010) published by the NCI's Clinical Proteomic Technologies for Cancer (CPTC)

  • Alexey Nesvizhskii has been named the Rising Young Investigator by Genome Technology magazine (January 2007 issue). See the article about Dr. Nesvizhskii titled "From Physics to Proteins", and the description of this award, here.

  • Dr. Nesvizhskii's research on the PeptideAtlas database, and motivation behind it, has been profiled in the publication in Genetic Engineering and Biotechnology News "Expansion of Proteomic databases Needed".

Our educational efforts

    Upcoming or recent summer schools, short courses, and tutorial lectures

  • 2012 CSHL Course on Proteomics
    July 7- July 22, 2012 Cold Spring Harbor, New York
    Alexey Nesvizhskii will teach a workshop on the analysis of AP-MS protein-protein interaction data (July 19)

  • 2012 US HUPO short course: Stable and Transient Protein-Protein Interactions: Discovery, Quantification and Validation
    March 4, 2012 San Francisco, California
    Instructors: Ileana Cristea, Alexey Nesvizhskii
    Offered first time at US HUPO. This course will cover fundamental and practical aspects of studying protein interactions, from experimental design to data analysis.

  • 2012 ASMS short course: Bioinformatics for Protein Identification
    May 19-20, 2012 Vancouver, Canada
    Instructors: Alexey Nesvizhskii, David Tabb, Nuno Bandiera
    The course presented at ASMS 2011 in Denver was well attended, so it is offered again. The course seeks to familiarize proteomics researchers with the inner workings of the software that enables this field. The course will emphasize the key steps in protein identification: peptide-spectrum matching, error rate estimation, and protein assembly. It will build on these topics by discussing nonconventional MS/MS identification, comparative proteomics, and manual verification.

  • Summer School in Systems Biology of Neurodegenerative Disease and China Canada Systems Biology Symposium and 19th Methods in Protein Structure Analysis (MPSA)
    June 18 - 27, 2012 Ottawa, Canada
    Course coordinators: Steffany Bennett and Daniel Figeys, Ottawa Institute of Systems Biology
    The school offers a unique 8 day intensive training in systems biology with focus on training scientists to overcome some of the challenges facing our understanding and treatment of intractable neurodegenerative disease. The lectures include a computational primer on the analysis and extraction of biological information from complex proteomics dataset. The full syllabus (Fall 2011 school) can be found here:

  • Past events

  • Alexey Nesvizhskii gave an overview on quantitative proteomics at the 2010 ASMS Conference in Salt Lake City, Utah in a section organized by Mike Washburn. He also lead with David Tabb a discussion at the Computational Mass Spectrometry/Bioinformatics for MS ASMS Interest Group Meeting (Wednesday, May 25) organized by Hanno Steen and Marc Kirchner.

  • Alexey Nesvizhskii presented two lectures at the Summer School on Computational Mass Spectrometry Based Proteomics at the Max Planck Institute of Biochemistry, Martinsried (near Munich, Germany), organized by Matthias Mann lab, 13-18 June 2010.

  • Alexey Nesvizhskii participated as aa guest speaker and instructor at NHLBI Proteomics and Genomics Workshop at the University of Colorado Denver, organized by Nichole Reisdorph and colleagues. June 23-July 2, 2010.

  • Watch Dr. Nesvizhskii on YouTube speaking about his research on Computational Methods for AP/MS Protein Interaction Data. Workshop "Understanding Protein Complexes, Networks and the Interactome" at the Case Center for Proteomics and Bioinformatics on November 10, 2009 (organized by Rob Ewing.

  • Alexey Nesvizhskii spoke at the International Minisymposium on "Quantitative Proteomics: A Central Technology for Systems Biology" held at the University of Zurich, Switzerland, on the October 30, 2009 organized by Erich Brunner and Christian Ahrens from the Systems Biology/Functional Genomics Center. For more information, please see the meeting report.

  • Alexey Nesvizhskii gave a tutorial lecture at the Workshop on Computational Proteomics at the Institute of Molecular and Cell Biology ( A-Star) in Singapore, December 3, 2009, organized by Walter Blackstock.

  • Watch a talk with an overview of Trans-Proteomic Pipeline, with a focus on PeptideProphet and ProteinProphet tools, given at Sage-N Research Annual User Meeting. Sage-N is one of the companies that distribute TPP as a part of their commercial system.