{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T14:56:04Z","timestamp":1761058564802},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS\/MS) database searching. However, these methods cannot identify proteins that are not already listed in existing databases. Moreover, the alternative approach of <jats:italic>de novo<\/jats:italic> sequencing requires costly equipment and the interpretation of complex MS\/MS spectra. Thus, there is a need for novel high-throughput protein-identification methods that are independent of existing predefined protein databases.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here, we present a hybrid method for genome-fingerprint scanning, known as HybGFS. This technique combines genome sequence-based peptide MS\/MS ion searching with liquid-chromatography elution-time (LC-ET) prediction, to improve the reliability of identification. The hybrid method allows the simultaneous identification and mapping of proteins without <jats:italic>a priori<\/jats:italic> information about their coding sequences. The current study used standard LC-MS\/MS data to query an <jats:italic>in silico<\/jats:italic>-generated six-reading-frame translation and the enzymatic digest of an entire genome. Used in conjunction with precursor\/product ion-mass searching, the LC-ETs increased confidence in the peptide-identification process and reduced the number of false-positive matches. The power of this method was demonstrated using recombinant proteins from the <jats:italic>Escherichia coli<\/jats:italic> K12 strain.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The novel hybrid method described in this study will be useful for the large-scale experimental confirmation of genome coding sequences, without the need for transcriptome-level expression analysis or costly MS database searching.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-479","type":"journal-article","created":{"date-parts":[[2006,10,31]],"date-time":"2006-10-31T07:14:52Z","timestamp":1162278892000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["HybGFS: a hybrid method for genome-fingerprint scanning"],"prefix":"10.1186","volume":"7","author":[{"given":"Kosaku","family":"Shinoda","sequence":"first","affiliation":[]},{"given":"Nozomu","family":"Yachie","sequence":"additional","affiliation":[]},{"given":"Takeshi","family":"Masuda","sequence":"additional","affiliation":[]},{"given":"Naoyuki","family":"Sugiyama","sequence":"additional","affiliation":[]},{"given":"Masahiro","family":"Sugimoto","sequence":"additional","affiliation":[]},{"given":"Tomoyoshi","family":"Soga","sequence":"additional","affiliation":[]},{"given":"Masaru","family":"Tomita","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,10,29]]},"reference":[{"key":"1218_CR1","doi-asserted-by":"publisher","first-page":"5011","DOI":"10.1073\/pnas.90.11.5011","volume":"90","author":"WJ Henzel","year":"1993","unstructured":"Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C: Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. 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