Validation of peptide and PTM identifications by chemical perturbation proteomics

Jakob Bunkenborg, Lasse Gaarde Falkenby, Lea Mørch Harder, Jens S. Andersen

Research output: Contribution to conference without publisher/journalPosterResearch

Abstract

Identification and characterization of proteins via database searching of tandem mass spectrometry data of peptides has become a central technique in proteomics. The massive amount of data generated precludes manual interpretation and validation of the identifications. The current standard procedure is repeating experiments and estimating false discovery rates by searching reverse or garbled protein sequence databases. One danger of this approach is that erroneous assignments can be made quite consistently and reproducibly by the software based on the measurement of a parent mass and the corresponding fragment ions. By derivatizing peptides the parent and fragment masses have to change consistently leading to non-redundant measurements. Here we explore chemical perturbation as a means of improving the confidence level of identifications.
Original languageEnglish
Publication date3. Jun 2011
Publication statusPublished - 3. Jun 2011
Event59th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics - Denver, CO, United States
Duration: 5. Jun 20119. Jun 2011
Conference number: 59

Conference

Conference59th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics
Number59
CountryUnited States
CityDenver, CO
Period05/06/201109/06/2011

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Pulse time modulation
Peptides
Mass spectrometry
Proteins
Ions
Experiments
Proteomics

Bibliographical note

ASMS 2011, Denver

Cite this

Bunkenborg, J., Falkenby, L. G., Harder, L. M., & Andersen, J. S. (2011). Validation of peptide and PTM identifications by chemical perturbation proteomics. Poster session presented at 59th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics, Denver, CO, United States.
Bunkenborg, Jakob ; Falkenby, Lasse Gaarde ; Harder, Lea Mørch ; Andersen, Jens S. / Validation of peptide and PTM identifications by chemical perturbation proteomics. Poster session presented at 59th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics, Denver, CO, United States.
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Bunkenborg, J, Falkenby, LG, Harder, LM & Andersen, JS 2011, 'Validation of peptide and PTM identifications by chemical perturbation proteomics', 59th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics, Denver, CO, United States, 05/06/2011 - 09/06/2011.

Validation of peptide and PTM identifications by chemical perturbation proteomics. / Bunkenborg, Jakob; Falkenby, Lasse Gaarde; Harder, Lea Mørch; Andersen, Jens S.

2011. Poster session presented at 59th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics, Denver, CO, United States.

Research output: Contribution to conference without publisher/journalPosterResearch

TY - CONF

T1 - Validation of peptide and PTM identifications by chemical perturbation proteomics

AU - Bunkenborg, Jakob

AU - Falkenby, Lasse Gaarde

AU - Harder, Lea Mørch

AU - Andersen, Jens S.

N1 - ASMS 2011, Denver

PY - 2011/6/3

Y1 - 2011/6/3

N2 - Identification and characterization of proteins via database searching of tandem mass spectrometry data of peptides has become a central technique in proteomics. The massive amount of data generated precludes manual interpretation and validation of the identifications. The current standard procedure is repeating experiments and estimating false discovery rates by searching reverse or garbled protein sequence databases. One danger of this approach is that erroneous assignments can be made quite consistently and reproducibly by the software based on the measurement of a parent mass and the corresponding fragment ions. By derivatizing peptides the parent and fragment masses have to change consistently leading to non-redundant measurements. Here we explore chemical perturbation as a means of improving the confidence level of identifications.

AB - Identification and characterization of proteins via database searching of tandem mass spectrometry data of peptides has become a central technique in proteomics. The massive amount of data generated precludes manual interpretation and validation of the identifications. The current standard procedure is repeating experiments and estimating false discovery rates by searching reverse or garbled protein sequence databases. One danger of this approach is that erroneous assignments can be made quite consistently and reproducibly by the software based on the measurement of a parent mass and the corresponding fragment ions. By derivatizing peptides the parent and fragment masses have to change consistently leading to non-redundant measurements. Here we explore chemical perturbation as a means of improving the confidence level of identifications.

M3 - Poster

ER -

Bunkenborg J, Falkenby LG, Harder LM, Andersen JS. Validation of peptide and PTM identifications by chemical perturbation proteomics. 2011. Poster session presented at 59th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics, Denver, CO, United States.