Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications

Brademan, Dain R.; Riley, Nicholas M.; Kwiecien, Nicholas W.; Coon, Joshua J.

doi:10.1074/mcp.tir118.001209

Cited by 128 publications

(121 citation statements)

References 45 publications

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“…Peptide outputs were processed using the Perseus (v1.4.0.6) 42 analysis environment to remove reverse matches and common protein contaminants with missing values imputed and the peptide intensities z-scored. MS/MS annotations were undertaken using the Interactive Peptide Spectral Annotator 43 . Mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD015752.…”

Section: Methodsmentioning

confidence: 99%

An intra-bacterial activity for a T3SS effector

Qaidi

Scott

Hays

et al. 2020

Sci Rep

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Many Gram-negative bacterial pathogens interact with mammalian cells by using type iii secretion systems (T3SS) to inject virulence proteins into host cells. A subset of these injected protein 'effectors' are enzymes that inhibit the function of host proteins by catalyzing the addition of unusual posttranslational modifications. The E. coli and Citrobacter rodentium NleB effectors, as well as the Salmonella enterica SseK effectors are glycosyltransferases that modify host protein substrates with N-acetyl glucosamine (GlcNAc) on arginine residues. This post-translational modification disrupts the normal functioning of host immune response proteins. T3SS effectors are thought to be inactive within the bacterium and fold into their active conformations after they are injected, due to the activity of chaperones that keep the effectors in a structural state permissive for secretion. While performing mass spectrometry experiments to identify glycosylation substrates of nleB orthologs, we unexpectedly observed that the bacterial glutathione synthetase (GshB) is glycosylated by NleB on arginine residue R256. NleB-mediated glycosylation of GshB resulted in enhanced GshB activity, leading to an increase in glutathione production, and promoted C. rodentium survival in oxidative stress conditions. these data represent, to our knowledge, the first intra-bacterial activity for a T3SS effector and show that arginine-GlcnAcylation, once thought to be restricted to host cell compartments, also plays an important role in regulating bacterial physiology.

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Section: Methodsmentioning

confidence: 99%

An intra-bacterial activity for a T3SS effector

Qaidi

Scott

Hays

et al. 2020

Sci Rep

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“…Despite the power of proteogenomics-driven MS/MS data integration in genome and metagenome annotation, peptide-spectral matches (PSMs) supporting novel proteoforms are prone to false positive identifications and usually require careful (and often manual) evaluation. Brademan et al (15) present IPSA, a web-based spectrum annotator that visualizes and characterizes peptide tandem mass spectra. ISPA can visualize peptides collected using a wide variety of experimental and instrumental configurations.…”

mentioning

confidence: 99%

Proteomics Is Not an Island: Multi-omics Integration Is the Key to Understanding Biological Systems

Zhang

Küster

2019

Molecular & Cellular Proteomics

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“…Alternatively, users may adjust the settings for specific annotated spectra according to the outputted images or preset the settings based on the visual effects using other visualization tools. Indeed, IPSA provided GUI for the annotation of a single spectrum but not for bulk processing of spectra annotation [8].…”

Section: Discussionmentioning

confidence: 99%

“…Currently, several tools are available to annotate and visualize the PSMs. MS-Viewer, pFind, xiSPEC, PeptideShaker, PRIDE Inspector and IPSA provide a graphical user interface (GUI) for comprehensively annotating and visualizing multiple spectra [8][9][10][11][12][13]. However, they do not support either mirror or alignment plots.…”

Section: Introductionmentioning

confidence: 99%

MMS2plot: an R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides

Ming

et al. 2020

Preprint

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A large number of post-translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot-gun proteomics datasets.Because the modified peptide fragments are low in abundance relative to the corresponding non-modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools would preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, we describe MMS2plot, an R package for visualizing peptide-spectrum matches (PSMs) for multiple peptides. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. We expect MMS2plot to play an important role in PTM discovery from large-scale proteomics datasets generated by LC (liquid chromatography)-MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL-3 license.

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Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications

Cited by 128 publications

References 45 publications

An intra-bacterial activity for a T3SS effector

An intra-bacterial activity for a T3SS effector

Proteomics Is Not an Island: Multi-omics Integration Is the Key to Understanding Biological Systems

MMS2plot: an R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides

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