Tandem Mass Spectrometry with Ultrahigh Mass Accuracy Clarifies

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Tandem Mass Spectrometry with Ultrahigh Mass Accuracy Clarifies Peptide Identification by Database Retrieval Michael T. Boyne II, Benjamin A. Garcia, Mingxi Li, Leonid Zamdborg, Craig D. Wenger, Shannee Babai, and Neil L. Kelleher* Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 Received August 13, 2008

A platform was developed to analyze MS/MS spectra from large peptides with low part-per-million mass accuracy, including a commercial-grade software suite. Termed Middle Down Proteomics, this platform identified 7454 peptides from 2-20 kDa (1472 unique) from 555 proteins after 23 LC-MS/MS injections of Lys-C digests of HeLa-S3 nuclear proteins. Along with greatly increased confidence for both peptide identification (expectation values from 10-89 to 10-4) and characterization (up to 18% of peptides were modified in some LC-MS/MS runs), fragmentation data with