Title: Support of Agilent Mass Spectrometers within the Skyline and Panorama Software Projects
Industry Gift from Agilent (PI: MacCoss)           5/1/2012 – 12/31/2024
We are continuing to extend our analytical software tools to support Agilent mass spectrometers.

Title: Support of SCIEX Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from SCIEX (PI: MacCoss)           1/1/2015 – 12/31/2024
We are continuing to extend our analytical software tools to support SCIEX mass spectrometers.

Title: Support of Shimadzu Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Shimadzu (PI: MacCoss)           1/15/2014 – 1/14/2025
We are continuing to extend our analytical software tools to support Shimadzu mass spectrometers.

Title: Support of Thermo Fisher Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Thermo Fisher (PI: MacCoss)           3/1/2014 – 2/28/2025
We are continuing to extend our analytical software tools to support Thermo Fisher mass spectrometers.

Title: Support of Waters Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Waters (PI: MacCoss)           9/1/2013 – 12/31/2024
We are continuing to extend our analytical software tools to support Waters mass spectrometers.

Prior Financial Support:

Title: Skyline Targeted Proteomics Environment
R01 GM103551 (PI: MacCoss)                9/14/2011 – 4/30/2021
The grant provided support for the continued development and maintenance of the widely used Skyline targeted proteomics software tool. It was superseded on 5/1/2021 by the Seattle Quant R24.

Title: Support of Bruker Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Bruker (PI: MacCoss)           8/1/2012 – 1/31/2024
We are continuing to extend our analytical software tools to support Bruker mass spectrometers.

Title: The Chorus Project: A Sustainable Cloud Solution for Mass Spectrometry Data
R01 GM121696 (PI: MacCoss)                      2/1/2016 – 1/31/2021
Large-scale mass spec file storage and pipeline processing. Replaced on 5/1/2021 by the Seattle Quant R24.

Title: Comprehensive Biology: Exploiting the Yeast Genome
P41 GM103533 (PI: MacCoss)                      9/1/2011 – 12/31/2022
This is a biotechnology resource center.  Dr. MacCoss’ role in the center is to develop quantitative mass spectrometry based technology for the measurement of protein dynamics.  This center will support training in the use of Skyline to the proteomics community. Furthermore, it supports the development of a webservices interface to access data within the Yeast Resource Center public data repository via Skyline.

Title: Library of Integrated Network-Based Cellular Signatures
U54 HG008097 (MPI: Jaffe)                7/1/2014 – 6/30/2020
This is a LINCS program grant to derive molecular signatures resultant from cellular perturbation.  We will develop a repository to disseminate multiplex mass spectrometry based assays via the Skyline client for use on all major mass spectrometry vendors.

Title: Self Correcting Nanoflow LC-MS for Clinical Proteomics
R01 GM107806 (PI: MacCoss)                                                            7/1/13 – 4/30/2017
The primary goal of this project is to improve the quality, reliability, and interlaboratory comparability of peptide mass spectrometry data. We are adding quality control capabilities to the Skyline software tool.  Furthermore, we are improving the interaction of Skyline with the instrument hardware and chromatography system.

Title: Data Acquisition and Analysis Strategies for Improving the Analysis of Peptide Mixtures Using Thermo Fisher Mass Spectrometers
Industry Sponsored Research Agreement (PI: MacCoss)           6/15/2010 – 6/15/2014
We are developing methods of analyzing mass spectrometry data on ThermoFisher mass spectrometers and Pierce reagents using Skyline.  This agreement is renewed yearly and we expect that the funding will be extended.

Title: Validating Protein Pathway Information – Integrating Proteomic Data with Transcriptomic or Metabolomic Data Sets
Industry Gift (PI: MacCoss)                                                              10/1/2011 - 9/31/2012
We are improving the interface between Agilent’s popular expression analysis software GeneSpring GX and Skyline.

Title: Genetic Regulation of Surfactant Deficiency
R01 HL082747 (PI: Cole  PI Subcontract: MacCoss)                        5/1/2011 – 3/31/2012
Goal was to understand the genetic and molecular mechanisms that disrupt pulmonary surfactant metabolism.  This project has supported the development of software and methodology for establishing targeted protein assays for Surfactant Protein-B.

Title: Label Free Differential Protein Analysis
University of Pittsburgh Contract                                                  7/1/2011 – 9/15/2011
Bridging funding to support the addition of label free MS1 quantitative analysis capabilities within Skyline.

Title: Clinical Proteomic Technology Assessment for Cancer (CPTAC)
U24 CA126479-S2 (PI: Liebler  PI Subcontract: MacCoss)               8/1/2009 – 7/31/2011
Funding provided to develop software to support the CPTAC centers for targeted proteomics method development and data analysis.