Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

Kenneth R. Durbin; John C. Tran; Leonid Zamdborg; Steve M M Sweet; Adam D. Catherman; Ji Eun Lee; Mingxi Li; John F. Kellie; Neil L. Kelleher

doi:10.1002/pmic.201000177

Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

Kenneth R. Durbin, John C. Tran, Leonid Zamdborg, Steve M M Sweet, Adam D. Catherman, Ji Eun Lee, Mingxi Li, John F. Kellie, Neil L. Kelleher^*

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

45 Scopus citations

Abstract

Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale.

Original language	English (US)
Pages (from-to)	3589-3597
Number of pages	9
Journal	Proteomics
Volume	10
Issue number	20
DOIs	https://doi.org/10.1002/pmic.201000177
State	Published - Oct 2010

Keywords

Bioinformatics
Data reduction
Deconvolution
Intact protein
Tandem MS/Top down

ASJC Scopus subject areas

Molecular Biology
Biochemistry

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10.1002/pmic.201000177

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abstract = "Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale.",

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author = "Durbin, {Kenneth R.} and Tran, {John C.} and Leonid Zamdborg and Sweet, {Steve M M} and Catherman, {Adam D.} and Lee, {Ji Eun} and Mingxi Li and Kellie, {John F.} and Kelleher, {Neil L.}",

year = "2010",

month = oct,

doi = "10.1002/pmic.201000177",

language = "English (US)",

volume = "10",

pages = "3589--3597",

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AU - Durbin, Kenneth R.

AU - Tran, John C.

AU - Zamdborg, Leonid

AU - Sweet, Steve M M

AU - Catherman, Adam D.

AU - Lee, Ji Eun

AU - Li, Mingxi

AU - Kellie, John F.

AU - Kelleher, Neil L.

PY - 2010/10

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N2 - Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale.

AB - Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale.

KW - Bioinformatics

KW - Data reduction

KW - Deconvolution

KW - Intact protein

KW - Tandem MS/Top down

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Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

Abstract

Keywords

ASJC Scopus subject areas

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