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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/251745
- author
- Levander, Fredrik
LU
and James, Peter
LU
- organization
- publishing date
- 2005
- 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 (ACS)
- external identifiers
-
- wos:000227287000007
- scopus:14844316045
- pmid:15707359
- 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
- 2016-04-01 12:05:56
- date last changed
- 2023-11-11 12:48:01
@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}},
keywords = {{protein identification; ion trap; time-of-flight; MALDI; AP-MALDI}},
language = {{eng}},
number = {{1}},
pages = {{71--74}},
publisher = {{The American Chemical Society (ACS)}},
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}},
doi = {{10.1021/pr0498584}},
volume = {{4}},
year = {{2005}},
}