OPTIMIZING SEARCH CONDITIONS FOR THE MASS FINGERPRINT-BASED ID OF PROTEINS
OPTIMIZING SEARCH CONDITIONS FOR THE MASS FINGERPRINT-BASED ID OF PROTEINS
批准号:
7954115
负责人:
David Fenyo
金额:
$0.36万
依托单位:
依托单位国家:
美国
项目类别:
财政年份:
2009
资助国家:
美国
项目状态:
已结题
起止时间:
2009-03-01 至 2010-02-28
关键词:
AlbuminsAlgorithmsAmino Acid SequenceClassificationCollectionComputer Retrieval of Information on Scientific Projects DatabaseDataFingerprintFundingGrantHumanInstitutionOutcomePeptide Sequence DeterminationPeptidesPlasmaPlasma ProteinsProbabilityProceduresProteinsProteomeReportingResearchResearch PersonnelResourcesSiteSourceTestingUnited States National Institutes of Healthbasehelix-loop-helix protein differentiation inhibitorimprovedmacromoleculeresearch study
中文摘要
这个子项目是众多研究子项目之一
英文摘要
This subproject is one of many research subprojects utilizing the
resources provided by a Center grant funded by NIH/NCRR. The subproject and
investigator (PI) may have received primary funding from another NIH source,
and thus could be represented in other CRISP entries. The institution listed is
for the Center, which is not necessarily the institution for the investigator.
The two central problems in protein identification by searching a protein sequence collection with MS data are the optimal use of experimental information to allow for identification of low abundance proteins and the accurate assignment of the probability that a result is false. For comprehensive MS-based protein identification, it is necessary to choose an appropriate algorithm and optimal search conditions. We report a systematic study of the quality of PMF-based protein identifications under different sequence collection search conditions using the Probability algorithm, which assigns the statistical significance to each result. We employed 2244 PMFs from 2-DE-separated human blood plasma proteins, and performed identification under various search constraints: mass accuracy (0.01-0.3 Da), maximum number of missed cleavage sites (0-2), and size of the sequence collection searched (5.6 x 10(4)-1.8 x 10(5)). By counting the number of significant results (significance levels 0.05, 0.01, and 0.001) for each condition, we demonstrate the search condition impact on the successful outcome of proteome analysis experiments. A mass correction procedure utilizing mass deviations of albumin matching peptides was tested in an attempt to improve the statistical significance of identifications and iterative searching was employed for identification of multiple proteins from each PMF.
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Protein Sequencing Tools for Biological Therapeutics
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批准号:8315630
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项目类别:
-
资助金额:$33.69万
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财政年份:2012
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负责人:David Fenyo
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依托单位:
Protein Sequencing Tools for Biological Therapeutics
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批准号:8731420
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项目类别:
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资助金额:$10.88万
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财政年份:2012
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负责人:David Fenyo
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依托单位:
Protein Sequencing Tools for Biological Therapeutics
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批准号:8979388
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项目类别:
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资助金额:$49.44万
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财政年份:2012
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负责人:David Fenyo
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依托单位:
Protein Sequencing Tools for Biological Therapeutics
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批准号:8539637
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项目类别:
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资助金额:$24.01万
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财政年份:2012
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负责人:David Fenyo
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依托单位:
AUTOMATIC PEAK FINDING AND DATABASE SEARCH USING RAW MALDI-LTQ-ORBITRAP DATA
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批准号:8361585
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项目类别:
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资助金额:$0.26万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
DETECTION AND CORRECTION OF INTERFERENCE IN MRM ANALYSIS
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批准号:8361582
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项目类别:
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资助金额:$0.39万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
STATISTICAL BASIS FOR DETERMINING SIGNIFICANCE OF LOCALIZATION OF MODIFICATIONS
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批准号:8361583
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项目类别:
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资助金额:$0.26万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
NEW WEB SITE CONSTRUCTION
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批准号:8361541
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项目类别:
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资助金额:$0.91万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
PROTEIN QUANTITATION USING MASS SPECTROMETRY
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批准号:8361557
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项目类别:
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资助金额:$1.04万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
IMPROVING THE SUCCESS RATE OF PROTEOME ANALYSIS
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批准号:8361523
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项目类别:
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资助金额:$0.26万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
DEVELOPED A VIEWER FOR CHIP-SEQ DATA
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批准号:8361546
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项目类别:
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资助金额:$0.13万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
ANALYSIS OF MASS-SPECTRA OF CROSS-LINKED PEPTIDES
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批准号:8361548
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项目类别:
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资助金额:$0.65万
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财政年份:2011
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负责人:David Fenyo
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依托单位:
INFORMATICS DEVELOPMENT: CHALLENGES AND SOLUTIONS FOR MALDI MASS SPECTROMETRY
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批准号:8169148
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项目类别:
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资助金额:$0.12万
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财政年份:2010
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负责人:David Fenyo
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依托单位:
DEVELOPED A VIEWER FOR CHIP-SEQ DATA
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批准号:8169175
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项目类别:
-
资助金额:$0.35万
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财政年份:2010
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负责人:David Fenyo
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依托单位:
NEW WEB SITE CONSTRUCTION
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批准号:8169170
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项目类别:
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资助金额:$0.35万
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财政年份:2010
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负责人:David Fenyo
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依托单位:
DEVELOPED SOFTWARE FOR ANALYSIS OF MASS-SPECTRA OF CROSS-LINKED PEPTIDES
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批准号:8169177
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项目类别:
-
资助金额:$0.23万
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财政年份:2010
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负责人:David Fenyo
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依托单位:
PROTEIN QUANTITATION USING MASS SPECTROMETRY
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批准号:8169186
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项目类别:
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资助金额:$1.16万
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财政年份:2010
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负责人:David Fenyo
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依托单位:
IMPROVING THE SUCCESS RATE OF PROTEOME ANALYSIS
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批准号:8169145
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项目类别:
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资助金额:$0.12万
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财政年份:2010
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负责人:David Fenyo
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依托单位:
NEW WEB SITE CONSTRUCTION
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批准号:7954139
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项目类别:
-
资助金额:$0.59万
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财政年份:2009
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负责人:David Fenyo
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依托单位:
DEVELOPED A VIEWER FOR CHIP-SEQ DATA
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批准号:7954144
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项目类别:
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资助金额:$0.36万
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财政年份:2009
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负责人:David Fenyo
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依托单位:
海外基金