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Comparison of protein expression lists from mass spectrometry of human blood fluids using exact peptide sequences versus BLAST

Abstract

The proteins in blood were all first expressed as mRNAs from genes within cells. There are databases of human proteins that are known to be expressed as mRNA in human cells and tissues. Proteins identified from human blood by the correlation of mass spectra that fail to match human mRNA expression products may not be correct. We compared the proteins identified in human blood by mass spectrometry by 10 different groups by correlation to human and nonhuman nucleic acid sequences. We determined whether the peptides or proteins identified by the different groups mapped to the human known proteins of the Reference Sequence (RefSeq) database. We used Structured Query Language data base searches of the peptide sequences correlated to tandem mass spectrometry spectra and basic local alignment search tool analysis of the identified full length proteins to control for correlation to the wrong peptide sequence or the existence of the same or very similar peptide sequence shared by more than one protein. Mass spectra were correlated against large protein data bases that contain many sequences that may not be expressed in human beings yet the search returned a very high percentage of peptides or proteins that are known to be found in humans. Only about 5% of proteins mapped to hypothetical sequences, which is in agreement with the reported false-positive rate of searching algorithms conditions. The results were highly enriched in secreted and soluble proteins and diminished in insoluble or membrane proteins. Most of the proteins identified were relatively short and showed a similar size distribution compared to the RefSeq database. At least three groups agree on a nonredundant set of 1671 types of proteins and a nonredundant set of 3151 proteins were identified by at least three peptides.

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Correspondence to Peihong Zhu or John Marshall.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Zhu, P., Bowden, P., Pendrak, V. et al. Comparison of protein expression lists from mass spectrometry of human blood fluids using exact peptide sequences versus BLAST. Clin Proteom 2, 185–203 (2006). https://doi.org/10.1007/BF02752500

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Key Words

  • Expression
  • analysis
  • proteomics
  • protein
  • composition
  • location
  • function
  • process
  • distribution
  • chi-square statistic
  • human
  • serum
  • LC/LC-MS/MS
  • computation