Publications

Prequips - An Extensible Software Platform for Integration, Visualization and Analysis of LC-MS/MS Proteomics Data

Nils Gehlenborg, Wei Yan, Inyoul Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, Leroy Hood, "Prequips - An Extensible Software Platform for Integration, Visualization and Analysis of LC-MS/MS Proteomics Data", Bioinformatics 25(5):682-683 (2009).

Description of the core software. Please cite this publication if you use Prequips in your work. A PDF of the preprint is available for download.

Abstract: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies.

An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures

Alexander Schmidt, Nils Gehlenborg, Bernd Bodenmiller, Lukas N Mueller, David Campbell, Markus Mueller, Ruedi Aebersold and Bruno Domon, "An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures", Molecular & Cellular Proteomics 7:2138-2150 (2008).

Description of the Inclusion List Builder plug-in for Prequips, which has been developed to make the generation of inclusion lists less time consuming, less prone to human error and easier to reproduce in directed LC-MS/MS approaches that decouple peak detection and sequencing of selected precursor ions.

Abstract: LC-MS/MS has emerged as the method of choice for the identification and quantification of protein sample mixtures. For very complex samples such as complete proteomes, the most commonly used LC-MS/MS method, data-dependent acquisition (DDA) precursor selection, is of limited utility. The limited scan speed of current mass spectrometers along with the highly redundant selection of the most intense precursor ions generates a bias in the pool of identified proteins toward those of higher abundance. A directed LC-MS/MS approach that alleviates the limitations of DDA precursor ion selection by decoupling peak detection and sequencing of selected precursor ions is presented. In the first stage of the strategy, all detectable peptide ion signals are extracted from high resolution LC-MS feature maps or aligned sets of feature maps. The selected features or a subset thereof are subsequently sequenced in sequential, non-redundant directed LC-MS/MS experiments, and the MS/MS data are mapped back to the original LC-MS feature map in a fully automated manner. The strategy, implemented on an LTQ-FT MS platform, allowed the specific sequencing of 2,000 features per analysis and enabled the identification of more than 1,600 phosphorylation sites using a single reversed phase separation dimension without the need for time-consuming prefractionation steps. Compared with conventional DDA LC-MS/MS experiments, a substantially higher number of peptides could be identified from a sample, and this increase was more pronounced for low intensity precursor ions.