Using dynamic programming to create isotopic distribution maps from mass spectra.

Using dynamic programming to create isotopic distribution maps from mass spectra. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Using dynamic programming to create isotopic distribution maps from mass spectra. Abstract Text:

Sean McIlwain,David Page,Edward L Huttlin,Michael R Sussman,

MOTIVATION: This article presents a method to identify the isotopic distributions within a mass spectrum using a probabilistic classifier supplemented with dynamic programming. Such a system is needed for a variety of purposes, including generating robust and meaningful features from mass spectra to be used in classification. RESULTS: The primary result of this article is that the dynamic programming approach significantly improves sensitivity, without harming specificity, of a probabilistic classifier for identifying the isotopic distributions. When annotating isotopic distributions where an expert has performed the initial 'peak-picking' (removal of noise peaks), the dynamic programming approach gives a true positive rate of 96% and a false positive rate of 0.0%, whereas the classifier alone has a true positive rate of only 47% when the false positive rate is 0.0%. When annotating isotopic distributions in machine peak-picked spectra, which may contain many noise peaks, the dynamic programming approach gives a true positive rate of only 22.0%, but it still keeps a low false positive rate of 1.0% and still outperforms the classifier alone. It is important to note that all these rates are when we require exact matches with the distributions in annotated spectra; in our evaluation a distribution is considered 'entirely incorrect' if it is missing even one peak or contains even one extraneous peak. We compared to the THRASH and AID-MS systems using a looser requirement: correctly identifying the distribution that contains the mono-isotopic mass. Under this measure, our dynamic programming approach achieves a true positive rate of 82% and a false positive rate of 1%, which again outperforms the classifier alone. The dynamic programming approach ends up being more conservative than THRASH and AID-MS, yielding both fewer true and false peaks, but the F-score of the dynamic programming approach is significantly better than those of THRASH and AID-MS. All results were obtained with 10-fold cross-validation of 99 sections of mass spectra with a total of 214 hand-annotated isotopic distributions. AVAILABILITY: Programs are available via http://www.cs.wisc.edu/~mcilwain/IDM.

Using dynamic programming to create isotopic distribution maps from mass spectra. Publishing Authors By Initials

S McIlwain,D Page,EL Huttlin,MR Sussman,

For similar investigative techniques: epidemiologic methods: statistics as topic: sensitivity and specificity research abstracts see: investigative techniques: epidemiologic methods: statistics as topic: sensitivity and specificity research

PUBMED ID PMID:

MEDLINE DATE:

Using dynamic programming to create isotopic distribution maps from mass spectra. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: i328-36

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 1

MONTH: Jul

YEAR: 2007

Using dynamic programming to create isotopic distribution maps from mass spectra. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9808944

Using dynamic programming to create isotopic distribution maps from mass spectra. Keywords Mesh Terms:

KEYWORDS: Sensitivity and Specificity

MESH TERMS: chemistry

Chemical & Substance for Abstract: Using dynamic programming to create isotopic distribution maps from mass spectra. Information

Substance Name: Radioisotopes

Registry Number: 0

Grant and Affiliation Information for Using dynamic programming to create isotopic distribution maps from mass spectra.

AFFILIATION: Department of Computer Sciences, University of Wisconsin, Madison, WI, USA. mcilwain@cs.wisc.edu

Country: England

AGENCY: United States NLM

GRANT: 5T15LM00739

ACRONYM: LM

MEDLINETA: Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Using dynamic programming to create isotopic distribution maps from mass spectra Related Publications

• "AKT"ing lessons for stem cells: regulation of cardiac myocyte and progenitor cell proliferation.
• 3-D structure of serum paraoxonase 1 sheds light on its activity, stability, solubility and crystallizability.
• AAHB Is the Mouthpiece of the Health Behavior Research Community.
• Acute hepatic dysfunction with abdominal pain and ascites.
• Agranulocytosis following the use of pyrithyldione; results of diagnostic test.
• American college of chest physicians consensus statement on the respiratory and related management of patients with duchenne muscular dystrophy undergoing anesthesia or sedation.
• Changing concepts of X-ray pelvimetry.
• Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana.
• Coning of spinal CT images in low back pain.
• Cost-effectiveness of multidisciplinary wound care in nursing homes: a pseudo-randomized pragmatic cluster trial.
• Differences in perceived implementation of a standard versus peer-led interactive substance abuse prevention program.
• Effects of bone meal on oral structures in pregnancy.
• Enhancement of penetration of penicillin into inflamed and normal mucous membrane by hyaluronidase.
• Fidelity of implementation in Project Towards No Drug Abuse (TND): a comparison of classroom teachers and program specialists.
• Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana.
• Interpreting antidepressant clinical trials.
• Peer acceleration: effects of a social network tailored substance abuse prevention program among high-risk adolescents.
• Perception of coarticulatory information in normal speech and dysarthria.
• Pim-1 regulates cardiomyocyte survival downstream of Akt.
• Plastic bowing fracture of the femur in a child.
• Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy.
• Renal lymphoma: spectrum of CT findings and potential mimics.
• Speech- and sound-segmentation in dyslexia: evidence for a multiple-level cortical impairment.
• Spontaneous infection of the brown dog tick, Rhipicephalus sanguineus with Coxiella burnetii.
• Stable isotope assisted assignment of elemental compositions for metabolomics.
• The 'chef's hat' appearance of the femoral head in cleidocranial dysplasia.
• Translating Science Into Service: Lessons Learned From the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) Study.
• Using dynamic programming to create isotopic distribution maps from mass spectra.
• Visual cues can modulate integration and segregation of objects in auditory scene analysis.
• [A new variety of Bardet-Biedl syndrome: external ophthalmoplegia, polydactylia, adiposogenital dystrophy, mental debility and hypoplasia of the hypothenar eminences.]