Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval

Michael T. Boyne; Benjamin A. Garcia; Mingxi Li; Leonid Zamdborg; Craig D. Wenger; Shannee Babai; Neil L. Kelleher

doi:10.1021/pr800635m

Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval

Michael T. Boyne, Benjamin A. Garcia, Mingxi Li, Leonid Zamdborg, Craig D. Wenger, Shannee Babai, Neil L. Kelleher

Molecular Biosciences

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

56 Scopus citations

Abstract

A platform was developed to analyze MS/MS spectra from large peptides with low part-per-million mass accuracy, including a commercial-grade software suite. Termed Middle Down Proteomics, this platform identified 7454 peptides from 2-20 kDa (1472 unique) from 555 proteins after 23 LC-MS/MS injections of Lys-C digests of HeLa-S3 nuclear proteins. Along with greatly increased confidence for both peptide identification (expectation values from 10 ^-89 to 10 ^-4) and characterization (up to 18% of peptides were modified in some LC-MS/MS runs), fragmentation data with <2 ppm accuracy enabled error tolerant and routine multiplexed database searching-all clearly demonstrated in this study.

Original language	English (US)
Pages (from-to)	374-379
Number of pages	6
Journal	Journal of Proteome Research
Volume	8
Issue number	1
DOIs	https://doi.org/10.1021/pr800635m
State	Published - Jan 2009

Keywords

High resolution
Human nuclei
Mass accuracy
Mass spectrometry
Post-translational modifications
Proteomics

ASJC Scopus subject areas

Chemistry(all)
Biochemistry

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10.1021/pr800635m

Cite this

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abstract = "A platform was developed to analyze MS/MS spectra from large peptides with low part-per-million mass accuracy, including a commercial-grade software suite. Termed Middle Down Proteomics, this platform identified 7454 peptides from 2-20 kDa (1472 unique) from 555 proteins after 23 LC-MS/MS injections of Lys-C digests of HeLa-S3 nuclear proteins. Along with greatly increased confidence for both peptide identification (expectation values from 10 -89 to 10 -4) and characterization (up to 18% of peptides were modified in some LC-MS/MS runs), fragmentation data with <2 ppm accuracy enabled error tolerant and routine multiplexed database searching-all clearly demonstrated in this study.",

keywords = "High resolution, Human nuclei, Mass accuracy, Mass spectrometry, Post-translational modifications, Proteomics",

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language = "English (US)",

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T1 - Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval

AU - Boyne, Michael T.

AU - Garcia, Benjamin A.

AU - Li, Mingxi

AU - Zamdborg, Leonid

AU - Wenger, Craig D.

AU - Babai, Shannee

AU - Kelleher, Neil L.

PY - 2009/1

Y1 - 2009/1

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AB - A platform was developed to analyze MS/MS spectra from large peptides with low part-per-million mass accuracy, including a commercial-grade software suite. Termed Middle Down Proteomics, this platform identified 7454 peptides from 2-20 kDa (1472 unique) from 555 proteins after 23 LC-MS/MS injections of Lys-C digests of HeLa-S3 nuclear proteins. Along with greatly increased confidence for both peptide identification (expectation values from 10 -89 to 10 -4) and characterization (up to 18% of peptides were modified in some LC-MS/MS runs), fragmentation data with <2 ppm accuracy enabled error tolerant and routine multiplexed database searching-all clearly demonstrated in this study.

KW - High resolution

KW - Human nuclei

KW - Mass accuracy

KW - Mass spectrometry

KW - Post-translational modifications

KW - Proteomics

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Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval

Abstract

Keywords

ASJC Scopus subject areas

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