Kenneth C. Parker

TL;DR: It is found that inactivation of Upf1p and Xrn1p causes common as well as unique effects on protein expression, and the use of 4-fold multiplexing to enable relative protein measurements simultaneously with determination of absolute levels of a target protein using synthetic isobaric peptide standards.

TL;DR: A new software program for the automated quantification of ICAT reagent labeled peptides analyzed by microcapillary electrospray ionization time-of-flight mass spectrometry determines those peptides that differ in their abundance.

TL;DR: Focusing on 14 spots in a narrow‐pH‐range gel, it is demonstrated how organizing peak‐table data and peptide match‐list data into databases enables the identification of a larger percentage of the peaks.

TL;DR: Protein scoring based on Combined Protein Score is orthogonal to many of the commonly used probability-based scoring schemes, and makes it possible to archive a more complete set of parameters that more thoroughly characterize the validity of the database match, which increases the confidence in the identifications.

TL;DR: This work sought to assess the reproducibility of peptide identification and to develop an informatics structure that characterizes the identification process as well as possible, especially with regard to tenuous identifications.