{"items":["60789479f6d9a50057bb6f86","6078931aac4e44005750a453","604f389b7d762a005e5c350c"],"styles":{"galleryType":"Columns","groupSize":1,"showArrows":true,"cubeImages":true,"cubeType":"max","cubeRatio":1.7777777777777777,"isVertical":true,"gallerySize":30,"collageAmount":0,"collageDensity":0,"groupTypes":"1","oneRow":false,"imageMargin":30,"galleryMargin":0,"scatter":0,"rotatingScatter":"","chooseBestGroup":true,"smartCrop":false,"hasThumbnails":false,"enableScroll":true,"isGrid":true,"isSlider":false,"isColumns":false,"isSlideshow":false,"cropOnlyFill":false,"fixedColumns":0,"enableInfiniteScroll":true,"isRTL":false,"minItemSize":50,"rotatingGroupTypes":"","rotatingCropRatios":"","columnWidths":"","gallerySliderImageRatio":1.7777777777777777,"numberOfImagesPerRow":3,"numberOfImagesPerCol":1,"groupsPerStrip":0,"borderRadius":0,"boxShadow":0,"gridStyle":0,"mobilePanorama":false,"placeGroupsLtr":true,"viewMode":"preview","thumbnailSpacings":4,"galleryThumbnailsAlignment":"bottom","isMasonry":false,"isAutoSlideshow":false,"slideshowLoop":false,"autoSlideshowInterval":4,"bottomInfoHeight":0,"titlePlacement":["SHOW_ON_THE_RIGHT","SHOW_BELOW"],"galleryTextAlign":"center","scrollSnap":false,"itemClick":"nothing","fullscreen":true,"videoPlay":"hover","scrollAnimation":"NO_EFFECT","slideAnimation":"SCROLL","scrollDirection":0,"scrollDuration":400,"overlayAnimation":"FADE_IN","arrowsPosition":0,"arrowsSize":23,"watermarkOpacity":40,"watermarkSize":40,"useWatermark":true,"watermarkDock":{"top":"auto","left":"auto","right":0,"bottom":0,"transform":"translate3d(0,0,0)"},"loadMoreAmount":"all","defaultShowInfoExpand":1,"allowLinkExpand":true,"expandInfoPosition":0,"allowFullscreenExpand":true,"fullscreenLoop":false,"galleryAlignExpand":"left","addToCartBorderWidth":1,"addToCartButtonText":"","slideshowInfoSize":200,"playButtonForAutoSlideShow":false,"allowSlideshowCounter":false,"hoveringBehaviour":"NEVER_SHOW","thumbnailSize":120,"magicLayoutSeed":1,"imageHoverAnimation":"NO_EFFECT","imagePlacementAnimation":"NO_EFFECT","calculateTextBoxWidthMode":"PERCENT","textBoxHeight":60,"textBoxWidth":200,"textBoxWidthPercent":75,"textImageSpace":10,"textBoxBorderRadius":0,"textBoxBorderWidth":0,"loadMoreButtonText":"","loadMoreButtonBorderWidth":1,"loadMoreButtonBorderRadius":0,"imageInfoType":"ATTACHED_BACKGROUND","itemBorderWidth":0,"itemBorderRadius":0,"itemEnableShadow":false,"itemShadowBlur":20,"itemShadowDirection":135,"itemShadowSize":10,"imageLoadingMode":"BLUR","expandAnimation":"NO_EFFECT","imageQuality":90,"usmToggle":false,"usm_a":0,"usm_r":0,"usm_t":0,"videoSound":false,"videoSpeed":"1","videoLoop":true,"jsonStyleParams":"","gallerySizeType":"px","gallerySizePx":1000,"allowTitle":true,"allowContextMenu":true,"textsHorizontalPadding":-30,"itemBorderColor":{"themeName":"color_12","value":"rgba(223,223,223,0)"},"showVideoPlayButton":true,"galleryLayout":2,"calculateTextBoxHeightMode":"MANUAL","targetItemSize":1000,"selectedLayout":"2|bottom|1|max|true|0|true","layoutsVersion":2,"selectedLayoutV2":2,"isSlideshowFont":true,"externalInfoHeight":60,"externalInfoWidth":0.75},"container":{"width":300,"galleryWidth":330,"galleryHeight":0,"scrollBase":0,"height":null}}
Dealing with NAs by bottom-up proteomic principle
Updated: Nov 25, 2020

We are pleased to present NAguideR, which is now online at Nucleic Acids Research (IF 11.15). https://doi.org/10.1093/nar/gkaa498.
Mass spectrometry (MS)-based quantitative proteomics experiments frequently generate data with missing values, which may profoundly affect downstream analyses. A wide variety of imputation methods have been established to deal with the missing-value issue. To date, however, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for proteomics community. Herein, we developed a user-friendly and powerful stand-alone software, NAguideR, to enable implementation and evaluation of different missing value methods offered by 23 widely used missing-value imputation algorithms. NAguideR further evaluates data imputation results through classic computational criteria and, unprecedentedly, proteomic empirical criteria, such as quantitative consistency between different charge-states of the same peptide, different peptides belonging to the same proteins, and individual proteins participating protein complexes and functional interactions. We applied NAguideR into three label-free proteomic datasets featuring peptide-level, protein-level, and phosphoproteomic variables respectively, all generated by data independent acquisition mass spectrometry (DIA-MS) with substantial biological replicates. The results indicate that NAguideR is able to discriminate the optimal imputation methods that are facilitating DIA-MS experiments over those sub-optimal and low-performance algorithms. NAguideR further provides downloadable tables and figures supporting flexible data analysis and interpretation.