Category Archives: 2011

Proteome identification using peptide-centric proteomics techniques is a routinely used analysis technique. One of the most powerful and popular methods for the identification of peptides from MS/MS spectra is protein database matching using search engines. Significance thresholding through false discovery … Continue reading →

We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances … Continue reading →

Mass spectrometry has become the method of choice for studying proteins in complex mixtures in a qualitative and quantitative fashion. The application of mass spectrometry-based proteomics analyses on plasma has correspondingly been established as an important method for disease-associated biomarker … Continue reading →

Mass spectrometry-based proteomics has become an essential part of the analytical toolbox of the life sciences. With the ability to identify and quantify hundreds to thousands of proteins in high throughput, the field has contributed its fair share to the … Continue reading →

The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library … Continue reading →

Initiation of protein translation is a well studied fundamental process, albeit high-throughput and more comprehensive determination of the exact translation initiation sites (TIS) was only recently made possible following the introduction of positional proteomics techniques that target protein N-termini. Precise … Continue reading →

Mass spectrometry-driven proteomics is increasingly relying on quantitative analyses for biological discoveries. As a result, different methods and algorithms have been developed to perform relative or absolute quantification based on mass spectrometry data. One of the most popular quantification methods … Continue reading →

Proteins are reckoned to be the key actors in a living organism. By studying proteins, one engages into deciphering a complex series of events occurring during a protein’s life span. This starts at the creation of a protein, which is … Continue reading →

MS-driven proteomics has evolved over the past two decades to a high tech and high impact research field. Two distinct factors clearly influenced its expansion: the rapid growth of an arsenal of instrument and proteomic techniques that led to an … Continue reading →

We here describe a normalization method to combine quantitative proteomics data. By merging the output of two popular quantification software packages, we obtained a 20% increase (on average) in the number of quantified human proteins without suffering from a loss … Continue reading →