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Reproducibility of tryptic digestion investigated by quantitative fourier transform ion cyclotron resonance mass spectrometry

Hagman, C; Ramstrom, M; Bentz, Maria LU ; James, Peter LU ; Hakansson, P and Bergquist, J (2005) In Journal of Proteome Research 4(2). p.394-399
Abstract
In this study, the reproducibility of tryptic digestion of complex solutions was investigated using liquid chromatography Fourier transform ion cyclotron resonance (LC FT-ICR) mass spectrometry. Tryptic peptides, from human cerebrospinal fluid, (CSF) were labeled with Quantification-Using-Enhanced-Signal-Tags (QUEST)-markers, or 1-([H-4]nicotinoyloxy)- and 1-([D-4]nicotinoyloxy)-succinimide ester markers. The analysis was performed on abundant proteins with respect-to-intensity ratios and sequence coverage and obtained by comparing differently labeled components from one or different pools. To interpret the dynamics in the proteome, one must be able to estimate the error introduced in each experimental steps. The intra sample variation due... (More)
In this study, the reproducibility of tryptic digestion of complex solutions was investigated using liquid chromatography Fourier transform ion cyclotron resonance (LC FT-ICR) mass spectrometry. Tryptic peptides, from human cerebrospinal fluid, (CSF) were labeled with Quantification-Using-Enhanced-Signal-Tags (QUEST)-markers, or 1-([H-4]nicotinoyloxy)- and 1-([D-4]nicotinoyloxy)-succinimide ester markers. The analysis was performed on abundant proteins with respect-to-intensity ratios and sequence coverage and obtained by comparing differently labeled components from one or different pools. To interpret the dynamics in the proteome, one must be able to estimate the error introduced in each experimental steps. The intra sample variation due to derivatization was approximately 10%. The inter sample variation depending on derivatization and tryptic digestion was not more than approximately 30%. These experimental observations provide a range for the up- and clown-regulations that are possible to study with electrospray ionization LC FT-ICR mass spectrometry. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
1-([D-4]nicotinoyloxy)-succinimide ester markers, 1-([H-4]nicotinoyloxy)- and, quantification, QUEST-markers, LC FT-ICR mass spectrometry, cerebrospinal fluid, tryptic reproducibility
in
Journal of Proteome Research
volume
4
issue
2
pages
394 - 399
publisher
The American Chemical Society
external identifiers
  • wos:000228421900022
  • scopus:17444416139
ISSN
1535-3893
DOI
10.1021/pr049809r
language
English
LU publication?
yes
id
54a7697c-3395-4b99-99a9-0d24ad803bd7 (old id 246390)
date added to LUP
2007-08-23 14:59:51
date last changed
2017-01-01 04:51:42
@article{54a7697c-3395-4b99-99a9-0d24ad803bd7,
  abstract     = {In this study, the reproducibility of tryptic digestion of complex solutions was investigated using liquid chromatography Fourier transform ion cyclotron resonance (LC FT-ICR) mass spectrometry. Tryptic peptides, from human cerebrospinal fluid, (CSF) were labeled with Quantification-Using-Enhanced-Signal-Tags (QUEST)-markers, or 1-([H-4]nicotinoyloxy)- and 1-([D-4]nicotinoyloxy)-succinimide ester markers. The analysis was performed on abundant proteins with respect-to-intensity ratios and sequence coverage and obtained by comparing differently labeled components from one or different pools. To interpret the dynamics in the proteome, one must be able to estimate the error introduced in each experimental steps. The intra sample variation due to derivatization was approximately 10%. The inter sample variation depending on derivatization and tryptic digestion was not more than approximately 30%. These experimental observations provide a range for the up- and clown-regulations that are possible to study with electrospray ionization LC FT-ICR mass spectrometry.},
  author       = {Hagman, C and Ramstrom, M and Bentz, Maria and James, Peter and Hakansson, P and Bergquist, J},
  issn         = {1535-3893},
  keyword      = {1-([D-4]nicotinoyloxy)-succinimide ester markers,1-([H-4]nicotinoyloxy)- and,quantification,QUEST-markers,LC FT-ICR mass spectrometry,cerebrospinal fluid,tryptic reproducibility},
  language     = {eng},
  number       = {2},
  pages        = {394--399},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Reproducibility of tryptic digestion investigated by quantitative fourier transform ion cyclotron resonance mass spectrometry},
  url          = {http://dx.doi.org/10.1021/pr049809r},
  volume       = {4},
  year         = {2005},
}