Reference Datasets

The RefData resource is a collection of publicly available mass spectrometry datasets (proteomics, metabolomics, lipidomics, etc.) for performance evaluation for a wide range of different methods, such as, for example data processing, quantiation, identification.

Title Description PubMed ID Repository ID
In-depth evaluation of software tools for data-independent acquisition based label-free quantification. Label-free quantification (LFQ) based on data-independent acquisition workflows currently experiences increasing popularity. Several software tools have been recently published or are commercially available. The present study focuses on the evaluation of three different software packages (Progenesis, synapter, and ISOQuant) supporting ion mobility enhanced data-independent acquisition data. In... 25545627 PXD001240
Latin Square Data A Latin Sqaure data set from the manuscript "SuperHirn - a novel tool for high resolution LC-MS based peptide/protein profiling". The available data spans the raw as well as preprocessed LC-MS runs (e.g. detected MS1 features), collected MS2 peptide identifications processed on the TransProteomicsPipeline (TPP) and the constructed MasterMaps. The dilution outline is perfomed over 6 LC-... 17726677
Metabolomics quantitation data sets The reference entry contains two datasets suitable for benchmarking feature-finding/quantification algorithms for LC-MS-based metabolomics. The first dataset (MTBL234) contains a spike-in experiment of selected compounds into a human plasma metabolome background. Seven different compounds (four of them with stable isotope labels) were added in a series of 10 concentrations covering four... 24176773 MTBLS234
Proteome informatics research group 2012: a study on detecting modified peptides in a complex mixture. The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community's ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring... 24187338 MSV000078492
SWATH-MS Gold Standard Dataset The SWATH-MS Gold Standard (SGS) dataset consists of 90 SWATH-MS runs of 422 synthetic stable isotope-labeled standard (SIS) peptides in ten different dilution steps, spiked into three protein backgrounds of varying complexity (water, yeast and human), acquired in three technical replicates. The SGS dataset was manually annotated, resulting in 342 identified and quantified peptides with three or... 24727770 PASS00289
Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective. Our data set compares: (i) SRM on a AB Sciex Qtrap 5500 (ii) SRM on a Thermo Scientific TSQ Vantage (iii) PRM on a Thermo Scientific Q Exactive (iv) DIA on an AB Sciex TripleTOF 5600 and (v) DIA on a Thermo Scientific Q Exactive HF. A pre-digested protein sample with a priori known analyte quantities (mixture of six trypsin-digested human proteins and 14 corresponding synthetic, heavy, stable... 27130639