Is there any way to enable/activate MSFragger and MS-GF+ without network access?
our skyline is installed offline without internet access, when first time MSFragger or MS-GF+, it ask to downlead or register, is there anyway to download offline?

When i used QuaSAR in Skyline, the following errors continue to occur.

"C:\Program Files\R\R-4.0.0\bin\R.exe" -f "C:\Users\msj0506\AppData\Local\Apps\2.0\W0DLG8VV.PHX\HHYW88CP.HLN\skyl..tion_e4141a2a22107248_0014.0001_a618d1d4217289b5\Tools\QuaSAR-2020.1\QuaSAR-Skyline.R" --slave --no-save --args "C:\Users\msj0506\AppData\Local\Apps\2.0\W0DLG8VV.PHX\HHYW88CP.HLN\skyl..tion_e4141a2a22107248_0014.0001_a618d1d4217289b5\Tools\QuaSAR-2020.1\QuaSAR.R" "C:\Users\msj0506\AppData\Local\Apps\2.0\W0DLG8VV.PHX\HHYW88CP.HLN\skyl..tion_e4141a2a22107248_0014.0001_a618d1d4217289b5\Tools\QuaSAR-2020.1\common.R" "C:\Users\msj0506\AppData\Local\Temp\QuaSAR_QuaSAR_Input.csv" NULL hhh "light Area" 1 "heavy Area" fmol/ul 1 1 -1 1 0 0 0 150 150 1 0.2 0 NULL hhh 0
[1] $Id: QuaSAR-Skyline.R 149 2014-10-23 13:56:13Z manidr $
[1] $Id: QuaSAR.R 149 2014-10-23 13:56:13Z manidr $
Error: package or namespace load failed for 'reshape' in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'C:/Users/msj0506/Documents/R/win-library/4.0/Rcpp/libs/x64/Rcpp.dll':
LoadLibrary failure: The specified procedure could not be found.
Execution halted
Finished!

What should I do if it keeps happening even if I reinstall it?

I attempted in May 26, 2020 to install QuaSAR (1_32) and work through the tutorial. I encountered the same error messages reported by jung165 (see p. 1of attached .ppt, Skyline support: QuaSAR download error, 2020-03-02, Nick Shulman responded on 2020-03-03).

We are running Skyline 20.1.0.76 (0d62152d0) with WIN 10 Enterprise Version 1809 (OS Build 17763.1217)

Screenshots are provided in the attached .ppt to facilitate asking of the following questions and illustrate the naive trouble shooting effort.

I am not an R programmer, but noticed that the R command used by Skyline to install the packages was going to an “http:” instead of an “https:” site.
Could the lack of the “s” prevent installation due to other security software running in the background?

Although it failed using R 3.0.1, using R 3.6.2, I was able to install the packages and their dependencies using the command.
o Install.packages(“bitops”, repos=”https:cran.us.r-project.org”)

This would seems to indicate the "missing S" hypothesis is wrong, but I don’t know enough R to move forward or know if this begins to address a larger problem, apparently still related to R 3.0.1. Is there a fix for this?

Thanks for any help you can provide to help get QuaSAR running again.

Hi, and thanks for taking a look at this.

I performed ID-MRM for four target peptides (3 transitions/peptide), with triplicate analyses at each of the 12 light peptide concentrations (2x-serial dilution series), at two matrix concentrations. This involved the use of 4 L-peptide sequences that were matched with the corresponding H-peptide sequences with AAA verification. The heavy peptide concentrations for different peptide target sequences were all slightly different from each other, although the spike level for individual H-peptides was the same in prepared samples for analysis. Double-blanks were used. Equal amounts of BSA were included in samples, prior to trypsin digest, as a digestion control. It is of interest to use QuaSAR to analyze the data.

The GenePattern QuaSAR Documentation indicates (p. 6) "...QuaSAR is unable to handle multiple concentrations for IS targets at this time." Does this mean I can't simply enter the different H-peptide spike levels, for the different peptides in the QuaSAR concentration map, and proceed?

What makes me worry is that:

• I've not been able to edit the document grid IS spike level for the different H-peptide sequences. When I change it for one peptide sequence, it changes for all the others.

• In the QuaSARInput report, I can't edit the H-peptide concentration/spike level to reflect the actual H-peptide concentrations for the different peptide sequences. If the edit .csv could then be processed by QuaSAR, maybe it would be a work around?

In the event QuaSAR can't handle multiple concentrations for IS targets, could I just perform the analysis using four different .sky documents, where I edit each of them to contain the correct H-spike concentrations? Maybe this is what the GenePattern QuaSAR Documentation was indicating on p. 4, and I just didn’t understand?

We're running Win7 Enterprise SP1, Skyline 4.2.0.19009 , and QuaSAR 1.32.

Thank you.

When going through the quasar doc,
https://skyline.ms/_webdav/home/software/Skyline/@files/tutorials/QuaSAR-1_4.pdf?listing=html

on pages 1-5, where talking about defining annotations, on bottom of page 1
"To create an annotation, perform the following steps:  On the Settings menu, click Annotations.  Press the Edit List button to bring up the Define Annotations form."

should be.....

To create an annotation, perform the following steps:  on the Settings menu, then click Document Settings... , then that brings up the define annotations.

-Sean