A Systematic Study into the Reproducibility of HPLC and Mass Spectrometry for the Analysis of Complex Protein Tryptic Digests by LC/MS

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Chris Hughes, Roy Martin, Therese McKenna, Iain Campuzano and Jim Langridge
Presented at: ABRF 2005; Association of Biomolecular Resource Facilities Annual Meeting; February 5-8; Savannah GA
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Previously it was shown that the relative quantification of peptides across samples can be accomplished by LC/MS, without the use of isotope labeling This paper shows the chromatographic and mass spectrometric reproducibility that can be obtained for the LC/MS analysis of complex peptide mixtures and the effect of these parameters on the matching of peptide ions between runs Automated algorithms were used to compare and contrast the peptide ions that could be matched across multiple injections Finally, a comparison was done of LC/MS data acquired at mass resolutions of >10000 FWHMand >17500 FWHM

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