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Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments

Levander, Fredrik LU and James, Peter LU (2005) In Journal of Proteome Research 4(1). p.71-74
Abstract
The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the... (More)
The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
protein identification, ion trap, time-of-flight, MALDI, AP-MALDI
in
Journal of Proteome Research
volume
4
issue
1
pages
71 - 74
publisher
The American Chemical Society
external identifiers
  • wos:000227287000007
  • scopus:14844316045
ISSN
1535-3893
DOI
10.1021/pr0498584
language
English
LU publication?
yes
id
c3671c44-7b76-4f13-bb2e-f0eaecfb2ec2 (old id 251745)
date added to LUP
2007-08-03 12:29:09
date last changed
2017-01-01 04:50:04
@article{c3671c44-7b76-4f13-bb2e-f0eaecfb2ec2,
  abstract     = {The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.},
  author       = {Levander, Fredrik and James, Peter},
  issn         = {1535-3893},
  keyword      = {protein identification,ion trap,time-of-flight,MALDI,AP-MALDI},
  language     = {eng},
  number       = {1},
  pages        = {71--74},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments},
  url          = {http://dx.doi.org/10.1021/pr0498584},
  volume       = {4},
  year         = {2005},
}