xiSPEC: web-based visualization, analysis and sharing of proteomics data

Kolbowski, Lars; Combe, Colin; Rappsilber, Juri

doi:10.1093/nar/gky353

Cited by 42 publications

(39 citation statements)

References 27 publications

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“…The ptm RS node was set to ignore neutral loss ions, and the “treat all spectra as EThcD” option was selected for EThcD data. Manual annotation was performed with the help of xiSPEC (Kolbowski et al , ).…”

Section: Methodsmentioning

confidence: 99%

Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation

et al. 2019

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Phosphorylation is a key regulator of protein function under (patho)physiological conditions, and defining site‐specific phosphorylation is essential to understand basic and disease biology. In vertebrates, the investigative focus has primarily been on serine, threonine and tyrosine phosphorylation, but mounting evidence suggests that phosphorylation of other “non‐canonical” amino acids also regulates critical aspects of cell biology. However, standard methods of phosphoprotein characterisation are largely unsuitable for the analysis of non‐canonical phosphorylation due to their relative instability under acidic conditions and/or elevated temperature. Consequently, the complete landscape of phosphorylation remains unexplored. Here, we report an unbiased phosphopeptide enrichment strategy based on strong anion exchange (SAX) chromatography (UPAX), which permits identification of histidine (His), arginine (Arg), lysine (Lys), aspartate (Asp), glutamate (Glu) and cysteine (Cys) phosphorylation sites on human proteins by mass spectrometry‐based phosphoproteomics. Remarkably, under basal conditions, and having accounted for false site localisation probabilities, the number of unique non‐canonical phosphosites is approximately one‐third of the number of observed canonical phosphosites. Our resource reveals the previously unappreciated diversity of protein phosphorylation in human cells, and opens up avenues for high‐throughput exploration of non‐canonical phosphorylation in all organisms.

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Section: Methodsmentioning

confidence: 99%

Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation

et al. 2019

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“…Peptide confidence was determined using Percolator [ 32 ] algorithm with a target value of 1% false discovery rate. As a result, the neopeptides MKANPALTM and IHFLSLLNF were discovered and visualized by xiSPEC [ 33 ], an interactive tool for visualizing and analyzing mass spectrometry data.…”

Section: Methodsmentioning

confidence: 99%

ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq

Zhang

Zhou

Tang

et al. 2020

Aging

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Cancer neoantigens have shown great potential in immunotherapy, while current software focuses on identifying neoantigens which are derived from SNVs, indels or gene fusions. Alternative splicing widely occurs in tumor samples and it has been proven to contribute to the generation of candidate neoantigens. Here we present ASNEO , which is an integrated computational pipeline for the identification of personalized Alternative Splicing based NEOantigens with RNA-seq. Our analyses showed that ASNEO could identify neopeptides which are presented by MHC I complex through mass spectrometry data validation. When ASNEO was applied to two immunotherapy-treated cohorts, we found that alternative splicing based neopeptides generally have a higher immune score than that of somatic neopeptides and alternative splicing based neopeptides could be a marker to predict patient survival pattern. Our identification of alternative splicing derived neopeptides would contribute to a more complete understanding of the tumor immune landscape. Prediction of patient-specific alternative splicing neopeptides has the potential to contribute to the development of personalized cancer vaccines.

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“…xiView uses xiSPEC 13 for the display of annotated spectra, including the option to view alternative explanations of the same spectrum. Like XLink-DB 2 (v2) and CLMSVault 5 , xiView uses xiNET 9 to display a 2D network of the crosslinks.…”

Section: Mainmentioning

confidence: 99%

xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry data

Graham

Combe

Kolbowski

et al. 2019

Preprint

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xiView provides a common platform for the downstream analysis and visualisation of Crosslinking Mass Spectrometry data. It is independent of the search software used and its input is compliant with the relevant mass spectrometry data standards. It uses established visualisation techniques, notably Multiple Coordinated Views, to help the user explore the data and is designed to facilitate comparisons between different datasets.

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xiSPEC: web-based visualization, analysis and sharing of proteomics data

Cited by 42 publications

References 27 publications

Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation

Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation

ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq

xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry data

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