Ultrafast ultraviolet photodissociation at 193 nm and its applicability to proteomic workflows

James A. Madsen, Daniel R. Boutz, Jennifer S. Brodbelt

Research output: Contribution to journalArticlepeer-review

100 Scopus citations


Ultraviolet photodissociation (UVPD) at 193 nm was implemented on a linear ion trap mass spectrometer for high-throughput proteomic workflows. Upon irradiation by a single 5 ns laser pulse, efficient photodissociation of tryptic peptides was achieved with production of a, b, c, x, y, and z sequence ions, in addition to immonium ions and v and w side-chain loss ions. The factors that influence the UVPD mass spectra and subsequent in silico database searching via SEQUEST were evaluated. Peptide sequence aromaticity and the precursor charge state were found to influence photodissociation efficiency more so than the number of amide chromophores, and the ion trap q-value and number of laser pulses significantly affected the number and abundances of diagnostic product ions (e.g., sequence and immonium ions). Also, photoionization background subtraction was shown to dramatically improve SEQUEST results, especially when peptide signals were low. A liquid chromatography-mass spectrometry (LC-MS)/UVPD strategy was implemented and yielded comparable or better results relative to LC-MS/collision induced dissociation (CID) for analysis of proteolyzed bovine serum albumin and lysed human HT-1080 cytosolic fibrosarcoma cells.

Original languageEnglish (US)
Pages (from-to)4205-4214
Number of pages10
JournalJournal of Proteome Research
Issue number8
StatePublished - Aug 6 2010


  • high-throughput
  • proteomics
  • tryptic peptides
  • ultraviolet photodissociation

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)


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