From 31118c989a864860cae9efe025e1e1bf4b86a979 Mon Sep 17 00:00:00 2001 From: adder Date: Wed, 6 Sep 2017 16:47:21 +0200 Subject: [PATCH] update reference --- README.md | 3 ++- docs/articles/bib.bib | 33 ++++++++++++++++++++++----------- docs/articles/saas.html | 38 ++++++++++++-------------------------- docs/index.html | 6 ++++-- vignettes/saas.Rmd | 16 ++++++++-------- 5 files changed, 48 insertions(+), 48 deletions(-) diff --git a/README.md b/README.md index a2fbadc..1695e2d 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,8 @@ An implementation of the Search All, Asses Subset strategy for FDR estimation in The search-all-assess-subset FDR procedure has been published in [Sticker et al. Nature Methods 14, 643–644 (2017) doi:10.1038/nmeth.4338](https://doi.org/10.1038/nmeth.4338) >Mass spectrometrists should search for all peptides, but assess only the ones they care about
>(Adriaan Sticker, Lennart Martens, Lieven Clement) -Please include this reference if you usesearch-all-assess-subset FDR procedure as part of a publication. + +Please include this reference if you use search-all-assess-subset FDR procedure as part of a publication. A user-friendly GUI version of saas is hosted [here](http://iomics.ugent.be/saas/). diff --git a/docs/articles/bib.bib b/docs/articles/bib.bib index 423bf11..9bc1583 100755 --- a/docs/articles/bib.bib +++ b/docs/articles/bib.bib @@ -218,14 +218,25 @@ @article{Vizcaino2016 volume = {44}, year = {2016} } -@article {Sticker2017, - author = {Sticker, Adriaan and Clement, Lieven and Martens, Lennart}, - title = {Mass spectrometrists should search for all peptides, but assess only the ones they care about}, - year = {2017}, - doi = {10.1101/094581}, - publisher = {Cold Spring Harbor Labs Journals}, - abstract = {In shotgun proteomics identified mass spectra that are deemed irrelevant to the scientific hypothesis are often discarded. Noble (2015) therefore urged researchers to remove irrelevant peptides from the database prior to searching to improve statistical power. We here however, argue that both the classical as well as Noble{\textquoteright}s revised method produce suboptimal peptide identifications and have problems in controlling the false discovery rate (FDR). Instead, we show that searching for all expected peptides, and removing irrelevant peptides prior to FDR calculation results in more reliable identifications at controlled FDR level than the classical strategy that discards irrelevant peptides post FDR calculation, or than Noble{\textquoteright}s strategy that discards irrelevant peptides prior to searching. We provide an implementation of our strategy as a user-friendly web-based tool at http://iomics.ugent.be/saas/.}, - URL = {http://biorxiv.org/content/early/2017/02/17/094581}, - eprint = {http://biorxiv.org/content/early/2017/02/17/094581.full.pdf}, - journal = {bioRxiv} -} \ No newline at end of file +@Comment @article {Sticker2017, +@Comment author = {Sticker, Adriaan and Clement, Lieven and Martens, Lennart}, +@Comment title = {Mass spectrometrists should search for all peptides, but assess only the ones they care about}, +@Comment year = {2017}, +@Comment doi = {10.1101/094581}, +@Comment publisher = {Cold Spring Harbor Labs Journals}, +@Comment abstract = {In shotgun proteomics identified mass spectra that are deemed irrelevant to the scientific hypothesis are often discarded. Noble (2015) therefore urged researchers to remove irrelevant peptides from the database prior to searching to improve statistical power. We here however, argue that both the classical as well as Noble{\textquoteright}s revised method produce suboptimal peptide identifications and have problems in controlling the false discovery rate (FDR). Instead, we show that searching for all expected peptides, and removing irrelevant peptides prior to FDR calculation results in more reliable identifications at controlled FDR level than the classical strategy that discards irrelevant peptides post FDR calculation, or than Noble{\textquoteright}s strategy that discards irrelevant peptides prior to searching. We provide an implementation of our strategy as a user-friendly web-based tool at http://iomics.ugent.be/saas/.}, +@Comment URL = {http://biorxiv.org/content/early/2017/02/17/094581}, +@Comment eprint = {http://biorxiv.org/content/early/2017/02/17/094581.full.pdf}, +@Comment journal = {bioRxiv} +@Comment } + +@Article{Sticker2017, + Author="Sticker, A. and Martens, L. and Clement, L. ", + Title="{{M}ass spectrometrists should search for all peptides, but assess only the ones they care about}", + Journal="Nat. Methods", + Year="2017", + Volume="14", + Number="7", + Pages="643--644", + Month="Jun" +} diff --git a/docs/articles/saas.html b/docs/articles/saas.html index a245383..d00fa0b 100644 --- a/docs/articles/saas.html +++ b/docs/articles/saas.html @@ -57,7 +57,7 @@

SAAS: Search All, Assess Subset

Adriaan Sticker

-

2017-05-04

+

2017-09-06

@@ -73,10 +73,9 @@

  • Remove all PSMs that match a protein you are not interesed in.
  • Calculate the FDR on the resulting subset of PSMs.
    • -

    A preprint of the manuscript on the search-all-assess FDR procedure can be found on bioRxiv (https://doi.org/10.1101/094581).

    -
    -

    Mass spectrometrists should search for all peptides, but assess only the ones they care about
    Adriaan Sticker, Lieven Clement, Lennart Martens (2017)

    -
    +

    The search-all-assess-subset FDR procedure has been published in Sticker et al. Nature Methods 14, 643–644 (2017) doi:10.1038/nmeth.4338.

    +

    Mass spectrometrists should search for all peptides, but assess only the ones they care about
    Adriaan Sticker, Lennart Martens, Lieven Clement (2017)

    +

    Please include this reference if you use search-all-assess-subset FDR procedure as part of a publication.

    False discovery rate (FDR) estimation

    @@ -375,13 +374,13 @@

    sessionInfo()

    sessionInfo()
    -
    ## R version 3.4.0 (2017-04-21)
+
    ## R version 3.4.1 (2017-06-30)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Arch Linux
 ## 
 ## Matrix products: default
-## BLAS: /usr/lib/libblas.so.3.7.0
-## LAPACK: /usr/lib/liblapack.so.3.7.0
+## BLAS: /usr/lib/libblas.so.3.7.1
+## LAPACK: /usr/lib/liblapack.so.3.7.1
 ## 
 ## locale:
 ## [1] C
@@ -389,24 +388,11 @@ 
    
 ## attached base packages:
 ## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
-## other attached packages:
-## [1] dplyr_0.5.0 saas_0.99.0
-## 
 ## loaded via a namespace (and not attached):
-##  [1] Rcpp_0.12.10        compiler_3.4.0      plyr_1.8.4         
-##  [4] ProtGenerics_1.8.0  tools_3.4.0         digest_0.6.12      
-##  [7] evaluate_0.10       tibble_1.3.0        gtable_0.2.0       
-## [10] shiny_1.0.3         DBI_0.6-1           yaml_2.1.14        
-## [13] parallel_3.4.0      stringr_1.2.0       knitr_1.15.1       
-## [16] hms_0.3             rprojroot_1.2       grid_3.4.0         
-## [19] cowplot_0.7.0       Biobase_2.36.0      R6_2.2.0           
-## [22] rmarkdown_1.5       ggplot2_2.2.1       readr_1.1.0        
-## [25] mzR_2.10.0          magrittr_1.5        backports_1.0.5    
-## [28] scales_0.4.1        codetools_0.2-15    htmltools_0.3.6    
-## [31] BiocGenerics_0.22.0 assertthat_0.2.0    mime_0.5           
-## [34] colorspace_1.3-2    xtable_1.8-2        httpuv_1.3.3       
-## [37] labeling_0.3        stringi_1.1.5       lazyeval_0.2.0     
-## [40] munsell_0.4.3       markdown_0.8
    
+##  [1] compiler_3.4.1  backports_1.1.0 magrittr_1.5    rprojroot_1.2  
+##  [5] tools_3.4.1     htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.12   
+##  [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.17      stringr_1.2.0  
+## [13] digest_0.6.12   evaluate_0.10.1

    @@ -422,7 +408,7 @@

    Elias, Joshua E, and Steven P Gygi. 2007. “Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.” Nature Methods 4 (3): 207–14. doi:10.1038/nmeth1019.

    -

    Sticker, Adriaan, Lieven Clement, and Lennart Martens. 2017. “Mass Spectrometrists Should Search for All Peptides, but Assess Only the Ones They Care About.” bioRxiv. Cold Spring Harbor Labs Journals. doi:10.1101/094581.

    +

    Sticker, A., L. Martens, and L. Clement. 2017. “Mass spectrometrists should search for all peptides, but assess only the ones they care about.” Nat. Methods 14 (7): 643–44.

    diff --git a/docs/index.html b/docs/index.html index 4be826c..92d7855 100644 --- a/docs/index.html +++ b/docs/index.html @@ -58,10 +58,12 @@

    search-all-assess-subset

    An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.

    -

    A preprint of the manuscript on the search-all-assess FDR procedure can be found on bioRxiv (https://doi.org/10.1101/094581).

    + +

    The search-all-assess-subset FDR procedure has been published in Sticker et al. Nature Methods 14, 643–644 (2017) doi:10.1038/nmeth.4338

    -

    Mass spectrometrists should search for all peptides, but assess only the ones they care about
    (Adriaan Sticker, Lieven Clement, Lennart Martens)

    +

    Mass spectrometrists should search for all peptides, but assess only the ones they care about
    (Adriaan Sticker, Lennart Martens, Lieven Clement)

    +

    Please include this reference if you usesearch-all-assess-subset FDR procedure as part of a publication.

    A user-friendly GUI version of saas is hosted here.

    More information on the FDR estimation procedure for subsets and the usage of the SAAS package can be found in the vignette

    diff --git a/vignettes/saas.Rmd b/vignettes/saas.Rmd index de3478b..73f9156 100644 --- a/vignettes/saas.Rmd +++ b/vignettes/saas.Rmd @@ -24,17 +24,17 @@ In short, the basic all-sub workflow comprises the following steps: 1. Remove all PSMs that match a protein you are not interesed in. 1. Calculate the FDR on the resulting subset of PSMs. -#A preprint of the manuscript on the search-all-assess FDR procedure can be found on bioRxiv ([https://doi.org/10.1101/094581](https://doi.org/10.1101/094581)). -# -#>Mass spectrometrists should search for all peptides, but assess only the ones they care about
    -#>Adriaan Sticker, Lieven Clement, Lennart Martens [-@Sticker2017] -# -The search-all-assess-subset FDR procedure has been published in [Sticker et al. Nature Methods 14, 643–644 (2017) doi:10.1038/nmeth.4338](https://doi.org/10.1038/nmeth.4338) + + + + + +The search-all-assess-subset FDR procedure has been published in [Sticker et al. Nature Methods 14, 643–644 (2017) doi:10.1038/nmeth.4338](https://doi.org/10.1038/nmeth.4338). Mass spectrometrists should search for all peptides, but assess only the ones they care about
    Adriaan Sticker, Lennart Martens, Lieven Clement [-@Sticker2017] -Please include this reference if you usesearch-all-assess-subset FDR procedure as part of a publication. +Please include this reference if you use search-all-assess-subset FDR procedure as part of a publication. ## False discovery rate (FDR) estimation Let $x$ be the PSM score and assume that larger score values indicate a better match to the theoretical spectrum. @@ -352,4 +352,4 @@ Note that none of the returned PSMs where sampled out of the incorrect target di sessionInfo() ``` -# References \ No newline at end of file +# References