Project description:MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool. Here, we present a comparative evaluation of six MS1-based quantification methods available in MQ and PD. Intensity (MQ and PD) and area (PD only) of the precursor ion peaks were measured and then subjected or not to normalization. The six methods were applied to datasets simulating various differential proteomics scenarios and covering a wide range of protein abundance ratios and concentrations. PD outperformed MQ in terms of quantification yield, dynamic range, and reproducibility, although neither platform reached a fully satisfactory quality of measurements at low-concentration ranges. PD methods including normalization were the most accurate in estimating the abundance ratio between groups and the most sensitive when comparing groups with a narrow abundance ratio; on the contrary, MQ methods generally reached slightly higher specificity, accuracy, and precision values. Moreover, we found that applying an optimized log ratio-based threshold can maximize specificity, accuracy, and precision. Taken together, these results can help researchers choose the most appropriate MS1-based protein quantification strategy for their studies.
Project description:Genome-wide location analysis of TAF1 and RNA polymerase II binding in ENCODE regions of IMR90, HCT116, HeLa and THP1 cell lines. There are a total of 8 experiments, each with three replicates. Details of chromatin immunoprecipitation and data analysis can be found at Li Z, van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B (2003) A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. PNAS, 100:8184-8169. Keywords: other
Project description:Pilot study on leaves from Papua New Guinea showing soil toxicity, extracted in RNAlater in one case and MQ water in another, also MQ blanks
Project description:This project contains raw data, intermediate files and results used to create the PRIDE human phosphoproteome map. The map is based on joint reanalysis of 110 publicly available human datasets. All relevant datasets were retrieved from the PRIDE database, and after manual curation, only assays that employed dedicated phospho-enrichment sample preparation strategies (e. g. metal oxide affinity chromatography, anti-P-Tyr antibodies, etc.) were included. Raw files were jointly processed with MaxQuant computational platform using standard settings (see Data Processing Protocol). In total, the joint analysis allowed identification of 252,189 phosphosites at 1% peptide spectrum match false discovery rate (PSM FDR) (MQ search results available in ‘txt-100PTM’ folder), of which 121,896 passed the additional 1% site localization FDR threshold (MQ search results available in ‘txt-001PTM’ folder).