Bioinformatics. 2007 Jan 15;23(2):264-5. Epub 2006 Nov 22.

PrepMS: TOF MS data graphical preprocessing tool.

Karpievitch YV, Hill EG, Smolka AJ, Morris JS, Coombes KR, Baggerly KA, Almeida JS.

Source

Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC 29425, USA. ykarpi@mdanderson.org

Abstract

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings, experimentally determined to work well in most situations. These values, if desired, can be changed by the user. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection and visual data quality assessment. AVAILABILITY: Stand-alone executable files and Matlab toolbox are available for download at: http://sourceforge.net/projects/prepms

PMID:: 17121773; [PubMed - indexed for MEDLINE]
PMCID:: PMC2633108

Free PMC Article

Images from this publication.See all images (1) Free text

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. [Bioinformatics. 2006]
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data.
Katajamaa M, Miettinen J, Oresic M. Bioinformatics. 2006 Mar 1; 22(5):634-6. Epub 2006 Jan 10.
HiRes--a tool for comprehensive assessment and interpretation of metabolomic data. [Bioinformatics. 2006]
HiRes--a tool for comprehensive assessment and interpretation of metabolomic data.
Zhao Q, Stoyanova R, Du S, Sajda P, Brown TR. Bioinformatics. 2006 Oct 15; 22(20):2562-4. Epub 2006 Aug 7.
The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. [Bioinformatics. 2007]
The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.
Salwinski L, Eisenberg D. Bioinformatics. 2007 Aug 15; 23(16):2193-5. Epub 2007 Jun 6.
Using the Proteomics Identifications Database (PRIDE). [Curr Protoc Bioinformatics. 2008]
Using the Proteomics Identifications Database (PRIDE).
Martens L, Jones P, Côté R. Curr Protoc Bioinformatics. 2008 Mar; Chapter 13:Unit 13.8.
Review Visualization techniques for genomic data. [Proc IEEE Comput Soc Bioinform...]
Review Visualization techniques for genomic data.
Loraine AE, Helt GA. Proc IEEE Comput Soc Bioinform Conf. 2002; 1:321-6.

See reviews... See all...

Cited by 9 PubMed Central articles

Automatic selection of preprocessing methods for improving predictions on mass spectrometry protein profiles. [AMIA Annu Symp Proc. 2010]
Automatic selection of preprocessing methods for improving predictions on mass spectrometry protein profiles.
Pelikan RC, Hauskrecht M. AMIA Annu Symp Proc. 2010 Nov 13; 2010:632-6. Epub 2010 Nov 13.
Linguistic approach for identification of medication names and related information in clinical narratives. [J Am Med Inform Assoc. 2010]
Linguistic approach for identification of medication names and related information in clinical narratives.
Hamon T, Grabar N. J Am Med Inform Assoc. 2010 Sep-Oct; 17(5):549-54.
Mass spectrometry-based analysis of therapy-related changes in serum proteome patterns of patients with early-stage breast cancer. [J Transl Med. 2010]
Mass spectrometry-based analysis of therapy-related changes in serum proteome patterns of patients with early-stage breast cancer.
Pietrowska M, Polanska J, Marczak L, Behrendt K, Nowicka E, Stobiecki M, Polanski A, Tarnawski R, Widlak P. J Transl Med. 2010 Jul 11; 8:66. Epub 2010 Jul 11.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

PrepMS: TOF MS data graphical preprocessing tool.
PrepMS: TOF MS data graphical preprocessing tool.
Bioinformatics. 2007 Jan 15 ;23(2):264-5. Epub 2006 Nov 22 .

PubMed
Control of endemic methicillin-resistant Staphylococcus aureus--recent advances ...
Control of endemic methicillin-resistant Staphylococcus aureus--recent advances and future challenges.
Clin Microbiol Infect. 2006 Dec ;12(12):1154-62.

PubMed
Patterns of sensitization in infants and its relation to atopic dermatitis.
Patterns of sensitization in infants and its relation to atopic dermatitis.
Pediatr Allergy Immunol. 2006 Dec ;17(8):591-600.

PubMed
What is the best approach to reducing birth defects associated with isotretinoin...
What is the best approach to reducing birth defects associated with isotretinoin?
PLoS Med. 2006 Nov ;3(11):e483.

PubMed
Mammalian inositol 3-phosphate synthase: its role in the biosynthesis of brain i...
Mammalian inositol 3-phosphate synthase: its role in the biosynthesis of brain inositol and its clinical use as a psychoactive agent.
Subcell Biochem. 2006 ;39:293-314.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to:

PrepMS: TOF MS data graphical preprocessing tool.

Source

Abstract

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

MeSH Terms

Substances

Grant Support

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Cited by 9 PubMed Central articles

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information