English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process

Wolski, W. E., Lalowski, M., Martus, P., Herwig, R., Giavalisco, P., Gobom, J., et al. (2005). Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics, 6, 285. doi:10.1186/1471-2105-6-285.

Item is

Files

show Files
hide Files
:
Wolski-2005-Transformation and o.pdf (Any fulltext), 502KB
Name:
Wolski-2005-Transformation and o.pdf
Description:
-
OA-Status:
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Locators

show

Creators

show
hide
 Creators:
Wolski, W. E.1, Author
Lalowski, M.1, Author
Martus, P.1, Author
Herwig, R.1, Author
Giavalisco, P.1, Author           
Gobom, J.1, Author
Sickmann, A.1, Author
Lehrach, H.1, Author
Reinert, K.1, Author
Affiliations:
1External Organizations, ou_persistent22              

Content

show
hide
Free keywords: Algorithms Analysis of Variance Animals Arabidopsis/genetics/metabolism Bacterial Proteins/chemistry Brain/metabolism Calibration Computational Biology/*methods *Data Interpretation, Statistical Mass Spectrometry/*methods Mice Models, Statistical Peptides/chemistry Proteins/chemistry ROC Curve Software
 Abstract: BACKGROUND: Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is called a peak-list. In order to classify the underlying amino acid sequence, the acquired spectra are usually compared with synthetic ones. Development of suitable methods of direct peak-list comparison may be advantageous for many applications. RESULTS: The pairwise peak-list comparison is a multistage process composed of matching of peaks embedded in two peak-lists, normalisation, scaling of peak intensities and dissimilarity measures. In our analysis, we focused on binary and intensity based measures. We have modified the measures in order to comprise the mass spectrometry specific properties of mass measurement accuracy and non-matching peaks. We compared the labelling of peak-list pairs, obtained using different factors of the pairwise peak-list comparison, as being the same or different to those determined by sequence database searches. In order to elucidate how these factors influence the peak-list comparison we adopted an analysis of variance type method with the partial area under the ROC curve as a dependent variable. CONCLUSION: The analysis of variance provides insight into the relevance of various factors influencing the outcome of the pairwise peak-list comparison. For large MS/MS and PMF data sets the outcome of ANOVA analysis was consistent, providing a strong indication that the results presented here might be valid for many various types of peptide mass measurements.

Details

show
hide
Language(s): eng - English
 Dates: 2005-11-302005
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: BMC Bioinformatics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 6 Sequence Number: - Start / End Page: 285 Identifier: -