High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples.

ABSTRACT: The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new UVPD fragmentation pathways in MassMatrix were rigorously and statistically optimized using two large data sets with high mass accuracy and high mass resolution for both MS(1) and MS(2) data acquired on an Orbitrap mass spectrometer for complex Halobacterium and HeLa proteome samples.

SUBMITTER: Madsen JA 

PROVIDER: S-EPMC3769333 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature