2004
DOI: 10.1074/mcp.r300012-mcp200
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Protein Identification by Mass Spectrometry

Abstract: During the past two decades, mass spectrometry has become established as the primary method for protein identification from complex mixtures of biological origin. This is largely attributable to the fortunate coincidence of instrumental advances that allow routine analysis of minute amounts (typically femtomoles) of involatile, polar compounds such as peptides in complex mixtures, with the rapid growth in genomic databases that are amenable to searching with mass spectrometry (MS) 1 data. Like many other dev… Show more

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Cited by 195 publications
(127 citation statements)
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“…The identified peptides receive a score and are combined into lists of identified proteins. A critical question in these experiments is what constitutes a reliable peptide and protein hit (2). Some laboratories save raw mass spectrometric data and interpret this raw data in all questionable cases.…”
Section: Mass Spectrometry (Ms)mentioning
confidence: 99%
“…The identified peptides receive a score and are combined into lists of identified proteins. A critical question in these experiments is what constitutes a reliable peptide and protein hit (2). Some laboratories save raw mass spectrometric data and interpret this raw data in all questionable cases.…”
Section: Mass Spectrometry (Ms)mentioning
confidence: 99%
“…Based on the experience gained from the large-scale genomics projects, there is widespread recognition that the proteomics field needs to invest early on in significant multi-laboratory efforts devoted to improving data quality [1], to making cross-laboratory and cross-platform data comparisons [2], and to developing data standards [3]. One such effort is the Plasma Proteomics Initiative, one of the first endeavors of the Human Proteome Organization Plasma Proteome Project (HUPO PPP) [4], which also includes liver and brain initiatives [5].…”
Section: Introductionmentioning
confidence: 99%
“…One of the most challenging problems nowadays concerns the correct interpretation of the large amount of data collected. Bioinformatics is capable of supporting proteomics in the interpretation of the data analysis and in the identification of the proteins of clinical interest by means of statistical analysis and use of algorithms (Baldwin, 2004). In fact, the discrepancy between reports from different authors may be due to the use of different database search software.…”
Section: Data Analysis and Protein Annotations In Seminal Plasma Protmentioning
confidence: 99%