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XTandem Explained

X!Tandem Theme. Central Axiom: For each identifiable protein, there is at least one detectable tryptic peptide.. X!Tandem Workflow. Quickly identify proteins from tryptic peptides.. Create databasecontaining identifiedproteins only.. Extensively searchfor modified/non-enzymaticpeptides only on identified proteins..

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XTandem Explained

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    1. X!Tandem Explained Brian C. Searle Proteome Software Inc. www.proteomesoftware.com 1336 SW Bertha Blvd, Portland OR 97219 (503) 244-6027 An explanation of the X!Tandem MS/MS spectra search program developed by Craig,R. and Beavis,R.C. (2003) Rapid Commun. Mass Spectrom., 17, 2310–2316.

    2. X!Tandem Theme Central Axiom: For each identifiable protein, there is at least one detectable tryptic peptide.

    3. X!Tandem Workflow

    4. X!Tandem’s Chief Advantage Speed: ~200x faster for nonspecific searches ~1000x faster if you also look for oxidation, deamidation, and phosphorylation

    5. Other X!Tandem Advantages Modern search techniques: Considers semi-tryptic peptides. Considers sequence polymorphisms. Uses probability-based scoring.

    6. Spectra

    7. Spectra matched

    8. Similar peaks

    9. Dot product

    10. Hyperscore

    11. Histogram of hyperscores

    12. Log histogram

    13. Significant scores

    14. E-value

    15. X!Tandem vs. SEQUEST

    16. Plotting SEQUEST and X!Tandem scores

    17. Cutoffs for SEQUEST and X!Tandem

    18. X!Tandem Summary X!Tandem is fast. The hyperscore is much faster to calculate than SEQUEST’s XCorr. This allows X!Tandem to build the histograms that allow it to calculate the E-values. X!Tandem grades on a curve. It’s the E-value that counts, not the hyperscore. X!Tandem and SEQUEST can often match different spectra.

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