Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility.

No abstract is available for this paper.

• Publication year

  2003

• Venue

  Analytical Chemistry

• Publication date

  2003-04-12

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1021/AC026424OPMID 12918992
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  1994cited by this paper
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