update reference

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<br/>
 >(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/).
 

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}
-}
+@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"
+}

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<br/>
-#>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)
+<!-- 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<br/> -->
+<!-- >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).
 
 Mass spectrometrists should search for all peptides, but assess only the ones they care about<br/>
 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
+# References