Welcome to the QuaSAR support board. If you have a question about using QuaSAR, or if you encounter a problem, you can post your questions here.

Support is provided by the creators of the software, as time allows, though we hope others will share their experience as the user community grows.

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Showing: all requestss
How to use Peptide Search without internet access
zhuhongbin321 2023-11-02 10:18

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?

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QuaSAR Error
msj0506 2020-06-28 23:28

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

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

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Fix provided for QuaSAR package installation failure: packages not available for R 3.0.1
(1 response) peter.scholl 2020-05-27 08:05

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 (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.

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peptide sequences with different H-peptide spike levels in matrix-matched std. curve
peter.scholl 2019-03-13 13:12

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 , and QuaSAR 1.32.

Thank you.

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quasar defining annotations edit
sponce1 2018-11-21 07:16

When going through the quasar doc,

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.


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QuaSAR error on Skyline
jung165 2018-04-10 17:47
Deal all,
I have a problem with running QuaSAR program on Skyline
I did triplicate run for response and non response about specific drug that I defined "SampleGroup" as R and NR, "Concentration" as 5 (which is 5ug of sample), and "IS Spike" as 200 (which is 200fmol/ul).

As unit of my sample and SIS peptides are different(ug and fmol/ul), Is it applicable to put values as I mentioned above??

Also, I have one more problem with running it. Below command is error on Skyline immediate window.
Any one can help??
I also attached my Skyline file.

Thank you

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: 'gplots'

The following object is masked from 'package:stats':


[1] >>> Processing part 1 of 1
[1] Initializing ...
[1] Running AuDIT ...
Error in run.AuDIT(file, output.prefix, required.columns = audit.required.columns, :
  Could not calculate any p values.
Calls: tryCatch ... eval -> tapply -> lapply -> FUN -> FUN -> run.AuDIT
Execution halted

 QuaSAR_error.skyd  QuaSAR_error.sky.view 
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Calculation of LOD
(1 response) carmen.gonzaleztejedo 2017-08-31 03:53
Does anyone know how QUASAR calculates the Limit of Detection? I am trying to reproduce the results on the excel sheet called "lod-lloq-raw", but I do know how to get the LOD given from the mean and sd values present in the same sheet.

Many thanks.
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Issues with the external tool quaSAR
Don Davis 2017-07-05 12:07
Hello all,

I am currently trying to perform some small molecule MRM data analysis using QuaSAR. However, I cannot make it through QuaSAR's tutorial with peptide data due to "Error: 'opts' is deprecated. Use 'theme' instead. (Defunct; last used in version 0.9.1) execution halted" which is found in the immediate window while executing QuaSAR. I've tried using all three versions of QuaSAR and still the same error. please help.


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Cannot install QuaSAR on 64-bit version
kathrin lauter4951 2017-01-18 03:09
Dear Skyline-Team,

I am trying to install the external Tool QuaSAR, but I always get an error (attached below) telling me that the system kannot find the required file.

I am working with the latest version of Skyline (64-bit version).

QuaSAR-1_32.zip is downloaded and then tried to be installed via the external tools-add from file.

It also does not work if installed "from tool store".

Can you help me?

Thanks a lot!!!

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Assay development
jdawlaty 2016-01-07 11:50
I am developing a PRM assay with 36 SI peptide standards. I need to determine the LOD, LOQ, make calibration curves for my standards. I do not have an additional internal standard. Is it possible to determine LOD, LOQ and make calibration curves using QuaSAR in Skyline for PRM data when no internal standard is present?
I have tried to follow the tutorial supplied but I think some things in Skyline have changed since the tutorial was written. The link to the QuaSAR documentation on page 8 of the tutorial is not working.
What is the purpose of the Sample Group? It seems to be the same grouping as the concentration.
After following the tutorial the PDF with the response curves that was generated did not open on my computer.
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Sum of transitions in version 1.32
laurapas 2015-07-14 15:20
I'm not seeing the sum of transitions with version 1.3.2, but it seems to be computed when using version 1.2. Will this be fixed in a later version? I haven't seen the code for version 1.2, but works with that older version. I run into an error with no resulting computed sum of transitions within the code block "if (calc.sum.tr)" in version 1.32.

I did my own temporary fix of "if (calc.sum.tr)", but notice that sums of transition is computed when the overall audit status = NA (i.e., p-value is NA and %CV = 0). Are NAs treated as "good"?
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QaSAR offline install
zhijcao 2015-04-01 11:15
Hi there,
    R has been installed in my computer. I try to offline install QaSAR, choose from file QaSAR.zip, but it still needs to access internet for R installer and package. is there any way to install QaRAR offline?
    Thank you
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"The system cannot find the path specified" for QuaSAR Tutorial
jie qian 2014-10-14 08:57
The QuaSAR tutorial package was downloaded and extracted to either desktop or document folder or C: disk. However, all locations give the same error message as "The system cannot find the path specified" in the immediate window.

Any suggestions?
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Error related to R installation for Quasar
daniel_spellman 2014-10-10 07:53
Has anyone else come accross this issue? I am recieving a series of errors while trying to intall quasar related the the version of R being installed.

Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/3.0
Warning message:
package 'bitops' is not available (for R version 3.0.1)
Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/3.0
Warning message:
package 'reshape' is not available (for R version 3.0.1)
Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/3.0
Warning message:
package 'gtools' is not available (for R version 3.0.1)
Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/3.0
Warning message:
package 'ggplot2' is not available (for R version 3.0.1)
Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/3.0
Warning message:
package 'gplots' is not available (for R version 3.0.1)
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Error running tutorial
(9 responses) nancy.finkel 2014-09-08 06:13
Hi. I am trying to run the tutorial and I am getting the following error message. Could you tell me what to do to fix this?


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Errors when running tutorial
(5 responses) wildsmith.kristin 2014-04-21 10:25
I am running through the Quasar tutorial with some colleagues and we are running into a couple problems with which i hope you can help. We have all just installed the Quasar tool in skyline and have encountered errors.
1.On my PC, Quasar give an error message (slide 1) that the required columns are missing, however, the results grid is complete.

2.On the second slide, all of us are missing the "standard present" box, and for my other 2 colleagues, Quasar runs, but no response curves are generated possibly due to an error with a specific peptide (see slide 3). We attempted to delete this peptide, but actually can't find it. It appears that all other plots and csv files were generated.
Do you have any suggestions for us?
 Quasar Errors.pptx 
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QuaSAR problem
(18 responses) <2166> 2014-02-25 00:50

We want to known how to calculate the LOD when heavy peptides are spiked in a matrix containing light peptides with unknown constant concentration.

In the panel QuaSAR, we want to use the option "none" in standard (because we don't know the concentration of light peptides)but we get an error message (joined ppt file)

Could you help us to use this option "none" and how to fill the IS spike column?

Best regards.

 error QuaSAR.pptx 
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