SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments

Abstract

Summary Mass spectrometry-based proteomics has had a formidable development in recent years, increasing the amount of data handled and the complexity of the statistical resources needed. Here we present SanXoT, an open-source, standalone software package for the statistical analysis of high-throughput, quantitative proteomics experiments. SanXoT is based on our previously developed weighted spectrum, peptide and protein statistical model and has been specifically designed to be modular, scalable and user-configurable. SanXoT allows limitless workflows that adapt to most experimental setups, including quantitative protein analysis in multiple experiments, systems biology, quantification of post-translational modifications and comparison and merging of experimental data from technical or biological replicates. Availability and implementation Download links for the SanXoT Software Package, source code and documentation are available at https://wikis.cnic.es/proteomica/index.php/SSP . Contact jvazquez@cnic.es or ebonzon@cnic.es Supplementary information Supplementary information is available at Bioinformatics online.

Lamin A/C deficiency in CD4+ T‐cells enhances regulatory T‐cells and prevents inflammatory bowel disease

“…Protein extraction and peptide identification were performed as described in refs 21 and 22, respectively. Functional analysis of the whole set of quantified proteins was performed using the systems biology triangle algorithm .…”

Programmed ‘disarming’ of the neutrophil proteome reduces the magnitude of inflammation

“…Quantitative information from TMT reporter intensities was integrated from the spectrum level to the peptide level, and then to the protein level based on the WSPP model using the Generic Integration Algorithm (GIA) 46,47 . Briefly, for the human experiment, for each sample i, the values x qps ¼ log 2 A i =C i I were calculated, where A i is the intensity of the TMT reporter of the 14:00 sample from the individual i in the MS/MS spectrum, s, coming from peptide, p, and protein, q, and C i is the intensity of the TMT reporter from the 8:00 sample from the same individual.…”

“…Protein quantifications where further integrated among the five comparisons in the human experiment, obtaining the averaged value In the mouse TMT experiments, for each sample i, the values x qps = log 2 A i /C i were calculated, where A i is the intensity of the TMT reporter from the individual i in the MS/MS spectrum, s, coming from peptide, p, and protein, q, and C i is the averaged intensity of the TMT reporters from all the samples in the given TMT experiment. The log 2 ratio of each peptide (x qp ) was calculated as the weighted mean of its spectra, the protein values (x q ) were the weighted mean of its peptides and the grand mean ( x I ) was calculated as the weighted mean of all the protein values 47 . The statistical weights of spectra, peptides and proteins (w qps , w qp and w q , respectively) and the variances at each one of the three levels (σ In all cases, protein abundance changes were then expressed in standardized units (Z q ), from which statistical significance of the changes in terms of the P value were calculated.…”

Molecular Characterization of the Coproduced Extracellular Vesicles in HEK293 during Virus-Like Particle Production

“…For the comparative analysis of the protein abundance changes, we applied the weighted scan peptide–protein (WSPP) statistical workflow, 26 using the SanXoT package. 27 It uses as an input a list of quantifications in the form of log2 ratios (for example, a condition versus control sample) with their statistical weights and generates the standardized forms of the original variables computing the quantitative values expressed in units of standard deviation around the averages. The quantitative information is obtained from the spectra and used to quantify the peptides from which the spectra are produced and, then, proteins that generate these peptides.…”