Author Archives: martlenn

iTRAQ protein quantification: A quality-controlled workflow

Reporter ion-based methods are among the major techniques to quantify peptides and proteins. Two main labels, tandem mass tag (TMT) and iTRAQ, are widely used by the proteomics community. They are, however, often applied as out-of-the-box methods, without thorough quality … Continue reading

Posted in 2011, Publications

A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods.

The identification of peptides and proteins from fragmentation mass spectra is a very common approach in the field of proteomics. Contemporary high-throughput peptide identification pipelines can quickly produce large quantities of MS/MS data that contain valuable knowledge about the actual … Continue reading

Posted in 2011, Publications

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called … Continue reading

Posted in 2011, Publications

compomics-utilities: an open-source Java library for computational proteomics

Background: The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a … Continue reading

Posted in 2011, Publications

Peptide Identification Quality Control

Identification of large proteomics datasets is routinely performed using sophisticated software tools called search engines. Yet despite the importance of the identification process, its configuration and execution is often performed according to established lab habits, and is mostly unsupervised by … Continue reading

Posted in 2011, Publications

A posteriori quality control for the curation and reuse of public proteomics data

Proteomics is a rapidly expanding field encompassing a multitude of complex techniques and data types. To date much effort has been devoted to achieving the highest possible coverage of proteomes with the aim to inform future developments in basic biology … Continue reading

Posted in 2011, Publications