Journal
JOURNAL OF PROTEOME RESEARCH
Volume 7, Issue 7, Pages 3054-3059Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr800169k
Keywords
mass spectrometry; neutral loss; cost function
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Funding
- Intramural NIH HHS [Z01 HL001285, Z01 HL001285-21, Z99 HL999999] Funding Source: Medline
- NHLBI NIH HHS [Z01-HL001285] Funding Source: Medline
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Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MSn). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS2 assignments from known synthetic data, > 98% agreement with an established MS2 assignment algorithm (Ascore), and >92% agreement with visual inspection of MS3 and MS4 spectra.
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