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Computational tools for top-down mass spectrometry based proteoform identification

Award Number: R01GM118470
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 06/01/2016
PERIOD OF PERFORMANCE END DATE: 08/31/2030

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Computational tools for top-down mass spectrometry based proteoform identification - PROJECT SUMMARY Mass spectrometry (MS)-based top-down proteomics has become one of the most informative approaches for proteoform analysis because it provides a bird’s-eye view of intact proteoforms with post-translational modifications. Database search and spectral library search are two approaches used for proteoform identification in top-down proteomics. While database search-based methods search query spectra against a protein/proteoform sequence database for identification, spectral library search-based methods first build a spectral library of proteoforms and then search query spectra against library spectra instead of protein/proteoform sequences for proteoform identification. In spectral library search, the query spectrum and the corresponding spectrum in the library are highly similar, giving spectral library search the potential to achieve higher sensitivity than database search in top-down MS-based proteoform identification. In this project, we propose to develop a new software package for proteoform identification using top-down spectral library search. Top-down spectral libraries are time consuming to build for non-model species, and deep learning-based top-down spectral prediction has the potential to build in silico top-down spectral libraries from protein sequences directly without MS experiments, facilitating the application of spectral libraries. In this project, we also propose to build deep learning ready top-down spectral libraries and use them to train deep learning models for top-down spectral prediction. In addition, annotation of top-down library spectra is a challenging problem due to the complexity of the spectra. We propose to develop new deep learning models to solve the charge state determination problem. The project has four specific aims. Aim 1: Develop the first software for identifying spectra with unknown mass shifts using top-down spectral library search. Aim 2: Build the first deep learning models for top-down mass spectral prediction. Aim 3: Develop the first proteoform-centric software for proteoform identification by top-down MS. Aim 4: Develop new deep learning models for automated charge state determination for top-down mass spectra. The project has a high impact. First, the project will yield a new software package and deep learning models for proteoform identification by top-down MS using spectral search. Second, the project will create top-down spectral libraries of model organisms and contribute to the human proteoform atlas. Third, the software tools and spectral libraries developed in the project will facilitate the identification of proteoform biomarkers in disease studies.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $329,097 )
2026	2026	THE ADMINISTRATORS OF TULANE EDUCATIONAL FUND	6823 SAINT CHARLES AVE	NEW ORLEANS	LA	70118	ORLEANS	USA	Biomedical Research and Research Training	001	10	8/31/2026	COMPETING CONTINUATION	$329,097
2026	2023	THE ADMINISTRATORS OF TULANE EDUCATIONAL FUND	6823 SAINT CHARLES AVE	NEW ORLEANS	LA	70118	ORLEANS	USA	Biomedical Research and Research Training	000	9	4/2/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $329,097

Issue Date FY: 2023 ( Subtotal = $294,904 )
2023	2023	ADMINISTRATORS OF THE TULANE EDUCATIONAL FUND, THE	6823 SAINT CHARLES AVE	NEW ORLEANS	LA	70118	ORLEANS	USA	Biomedical Research and Research Training	000	9	8/22/2023	NON-COMPETING CONTINUATION	$294,904
														Subtotal = $294,904

Issue Date FY: 2022 ( Subtotal = $282,462 )
2022	2022	ADMINISTRATORS OF THE TULANE EDUCATIONAL FUND, THE	6823 SAINT CHARLES AVE	NEW ORLEANS	LA	70118	ORLEANS	USA	Biomedical Research and Research Training	001	8	9/23/2022	NON-COMPETING CONTINUATION	$282,462
2022	2020	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	000	5	11/3/2021	COMPETING CONTINUATION	$0
														Subtotal = $282,462

Issue Date FY: 2021 ( Subtotal = $304,438 )
2021	2021	ADMINISTRATORS OF THE TULANE EDUCATIONAL FUND, THE	6823 SAINT CHARLES AVE	NEW ORLEANS	LA	70118	ORLEANS	USA	Biomedical Research and Research Training	003	7	9/22/2021	NON-COMPETING CONTINUATION	$287,090
2021	2020	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	001	5	9/3/2021	COMPETING CONTINUATION	-$275,190
2021	2020	ADMINISTRATORS OF THE TULANE EDUCATIONAL FUND, THE	6823 SAINT CHARLES AVE	NEW ORLEANS	LA	70118	ORLEANS	USA	Biomedical Research and Research Training	002	6	9/7/2021	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$292,538
2021	2019	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	000	4	7/3/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $304,438

Issue Date FY: 2020 ( Subtotal = $335,435 )
2020	2020	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	001	5	8/7/2020	COMPETING CONTINUATION	$335,435
2020	2019	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	000	4	7/30/2020	NON-COMPETING CONTINUATION	$0
														Subtotal = $335,435

Issue Date FY: 2019 ( Subtotal = $292,647 )
2019	2019	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	000	4	5/20/2019	NON-COMPETING CONTINUATION	$292,647
														Subtotal = $292,647

Issue Date FY: 2018 ( Subtotal = $291,852 )
2018	2018	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	000	3	5/24/2018	NON-COMPETING CONTINUATION	$291,852
														Subtotal = $291,852

Issue Date FY: 2017 ( Subtotal = $292,074 )
2017	2017	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	000	2	5/15/2017	NON-COMPETING CONTINUATION	$262,866
2017	2017	TRUSTEES OF INDIANA UNIVERSITY	980 INDIANA AVE RM 2232	INDIANAPOLIS	IN	46202	MARION	USA	Biomedical Research and Research Training	001	2	6/8/2017	NON-COMPETING CONTINUATION	$29,208
														Subtotal = $292,074

Issue Date FY: 2016 ( Subtotal = $299,451 )
2016	2016	INDIANA UNIVERSITY, BLOOMINGTON	509 EAST 3RD STREET	BLOOMINGTON	IN	47405	MONROE	USA	Biomedical Research and Research Training	000	1	5/27/2016	NEW	$299,451
														Subtotal = $299,451

Grand Total All Awards = $2,722,360

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Computational tools for top-down mass spectrometry based proteoform identification

Award Number: R01GM118470

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 06/01/2016

PERIOD OF PERFORMANCE END DATE: 08/31/2030

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