Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project

Journal of Proteome Research
Jin-Young ChoYoung-Ki Paik

Abstract

Approximately 2.9 billion long base-pair human reference genome sequences are known to encode some 20 000 representative proteins. However, 3000 proteins, that is, ∼15% of all proteins, have no or very weak proteomic evidence and are still missing. Missing proteins may be present in rare samples in very low abundance or be only temporarily expressed, causing problems in their detection and protein profiling. In particular, some technical limitations cause missing proteins to remain unassigned. For example, current mass spectrometry techniques have high limits and error rates for the detection of complex biological samples. An insufficient proteome coverage in a reference sequence database and spectral library also raises major issues. Thus, the development of a better strategy that results in greater sensitivity and accuracy in the search for missing proteins is necessary. To this end, we used a new strategy, which combines a reference spectral library search and a simulated spectral library search, to identify missing proteins. We built the human iRefSPL, which contains the original human reference spectral library and additional peptide sequence-spectrum match entries from other species. We also constructed the human simSPL, ...Continue Reading

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Citations

Jan 6, 2016·Mass Spectrometry Reviews·Han HuJoseph Zaia
Apr 8, 2016·Clinical and Translational Medicine·Björn L D M BrücherIjaz S Jamall
Jul 13, 2016·Mass Spectrometry Reviews·Wenguang Shao, Henry Lam
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Nov 21, 2018·Omics : a Journal of Integrative Biology·Qingwei MaWei Wang
Nov 26, 2016·Expert Review of Proteomics·Victor SeguraFernando J Corrales
Mar 4, 2021·Current Protocols·Srikanth S MandaQing Zhong
Dec 2, 2017·Journal of Proteome Research·Young-Ki PaikGilbert S Omenn
Aug 27, 2021·Journal of Molecular and Cellular Cardiology·Melinda WojtkiewiczRebekah L Gundry

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