Lab News

Mike wins Discovery in Proteomic Sciences Award from HUPO

posted Nov 9, 2016, 3:16 PM by Nat Brace   [ updated Nov 9, 2016, 3:34 PM ]

Professor Mike MacCoss awarded the HUPO Discovery in Proteomic Sciences Award for his developments in methodology and software for the quantitative analysis of complex protein mixtures. The focus of his lab is the development of high-throughput quantitative proteomic methods and their application to model organisms. To enable this research, Mike and his research team have developed a software program Skyline -- a free, openly available software package for the design and interpretation of targeted proteomics experiments -- which as had a remarkable impact and is widely adopted within the proteomics community.  This has placed Mike as a leader in the field of quantitative proteomics.

Graduate Student Lindsay Pino awarded Fellowship

posted Nov 9, 2016, 2:42 PM by Nat Brace

MacCoss Lab's Lindsay Pino was recently awarded a NRSA individual fellowship from the National Institutes of Health (NIH) for her ongoing research into molecular phenotyping of the yeast samples.  NRSA F31 grants, like Lindsay's, are awarded to promising predoctoral students enabling them to obtain individualized research training and mentorship from outstanding faculty sponsors in scientific health-related fields. 

Brendan MacLean wins inaugural Omenn Award

posted Nov 9, 2016, 2:20 PM by Nat Brace   [ updated Nov 9, 2016, 3:37 PM ]

Skyline Principal Developer Brendan MacLean  received the 2016 Gilbert S. Omenn Computational Proteomics Award from US HUPO.   This year, HUPO created a new award to recognize the specific achievements of a scientist or researcher who has developed software tools used by the proteomics community. In the announcement, HUPO highlighted the importance of and reliance on computational software which is sometimes under-recognized. This award is named in honor of Gil Omenn, a US HUPO Past President, leader of the Human Proteome Project, and influential proteomics researcher.

Since August, 2008 Brendan has worked as a the Principal Developer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community. Prior to that, Brendan made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline and was one of the founding partners and a key programmer of the Computational Proteomics Analysis System (CPAS) which would eventually become LabKey

New Perspective Paper Published in MCP

posted Aug 14, 2015, 5:28 PM by Michael MacCoss

Working with several proteomics labs, Sonia Ting put together a Perspective paper describing the Pros and Cons of Peptide-Centric analysis of mass spectrometry data.  This paper was recently highlighted in GenomeWeb.

Mike MacCoss is Awarded the 2015 Biemann Medal

posted Jul 6, 2015, 4:55 PM by Michael MacCoss   [ updated Jul 6, 2015, 4:56 PM ]

From the ASMS Website:

Dr. MacCoss has made a number of contributions of serious and long lasting impact to the field of proteomics. Chief among these is software development that has greatly facilitated proteomics. Dr. MacCoss’ philosophy on making software freely available and continually supporting this software so that it enables others has greatly benefitted the proteomic sciences. 

Bioinformatics tools developed by the MacCoss laboratory facilitate many different aspects of mass spectrometry data analysis. This includes tools for liquid chromatography mass spectrometry (LC-MS) feature finding, spectrum library searching, peak detection, post-processors for peptide database searching, and more. An important early contribution from his lab, the Percolator algorithm, improved peptide identifications from proteomic analyses through semi-supervised machine learning (Käll et al. “Semi-supervised learning for peptide identification from shotgun proteomics datasets,” Nature Methods, 2007). Percolator became widely adopted partially because of its use of a liberal open source license that encouraged companies to build on Percolator and incorporate into commercial packages (e.g. Mascot and Proteome Discoverer).  Another high-impact contribution from the MacCoss laboratory is the development and continued support of an integrated set of software tools called Skyline (MacLean et al. “Skyline: an open source document editor for creating and analyzing targeted proteomics experiments” Bioinformatics, 2010; available from Critically, Skyline is a vendor-neutral toolset, thus enabling methods to be easily transferred and tested across labs, even those that utilize different instrument platforms. Dr. MacCoss has also substantially advanced the new area of data-independent MS analyses. His key contribution in this area has been to develop a multiplexed strategy to better isolate noise and improve signal detection and therefore sensitivity through observational coherence (Egertson et al., Nature Methods 2013). 

One of the most recent projects championed by Dr. MacCoss is a nonprofit to provide a cost effective mechanism for labs to backup, share, visualize, and analyze data on the cloud called The Chorus Project ( They are working with developers in academic labs and companies to offer tools to our community that can process mass spectrometry data stored within Chorus.  The hope is to provide a platform where all labs have access to the latest analysis tools and published data can be easily reanalyzed.

Dr. MacCoss is professor in the Department of Genome Sciences, University of Washington, Seattle.

Photos from the Award Lecture can be found here.

Shared Proteomics Interview

posted Apr 29, 2014, 10:41 AM by Michael MacCoss

This was done a while ago but I'm just getting around to updating content on the website.  

Successful Targeted Protein Quantitation Course at UW

posted Apr 29, 2014, 10:35 AM by Michael MacCoss

We hosted an extremely successful course of targeted protein quantitation by mass spectrometry.  We had people from all of the world with diverse scientific backgrounds.  We were fortunate to have a great group of instructors who helped us put together this unique course material.  Our plan is to make this an annual event.  

Click here to see some photos.

New MCP Editorial on SRM Assays versus Western Blots

posted Jun 28, 2013, 4:16 PM by Michael MacCoss

We have been arguing this same thing for a long time.  Great to see this a focus of an editorial!

Viewing the Targeted Proteomics Horizon with Skyline

posted Jun 28, 2013, 4:12 PM by Michael MacCoss

The National Cancer Institute eProtein Newsletter highlights both Skyline and Panorama from the MacCoss Lab.

Multiplexed MS/MS for improved data-independent acquisition

posted Jun 28, 2013, 4:09 PM by Michael MacCoss

In mass spectrometry–based proteomics, data-independent acquisition (DIA) strategies can acquire a single data set useful for both identification and quantification of detectable peptides in a complex mixture. However, DIA data are noisy owing to a typical five- to tenfold reduction in precursor selectivity compared to data obtained with data-dependent acquisition or selected reaction monitoring. We demonstrate a multiplexing strategy, MSX, for DIA analysis that increases precursor selectivity fivefold.

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