https://skyline.ms MacCoss Lab Software: MacCoss Lab Software site https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=62791&_print=1 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? Thu Nov 02 10:18:01 PDT 2023 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=47691&_print=1 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? Sun Jun 28 23:28:15 PDT 2020 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=47358&_print=1 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. Wed May 27 08:05:21 PDT 2020 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=39317&_print=1 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. Wed Mar 13 13:12:00 PDT 2019 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=38207&_print=1 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 Wed Nov 21 07:16:29 PST 2018 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=36032&_print=1 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': lowess [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 Finished! Tue Apr 10 17:47:53 PDT 2018 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=31297&_print=1 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. Thu Aug 31 03:53:20 PDT 2017 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=30779&_print=1 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. Thanks, Don Wed Jul 05 12:07:59 PDT 2017 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=28299&_print=1 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!!! Kathrin Wed Jan 18 03:09:19 PST 2017 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=24928&_print=1 Hi, 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. Thu Jan 07 11:50:52 PST 2016 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=22537&_print=1 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"? Tue Jul 14 15:20:09 PDT 2015 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=20566&_print=1 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 zhijun Wed Apr 01 11:15:42 PDT 2015 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=15402&_print=1 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? Thanks. Tue Oct 14 08:57:40 PDT 2014 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=15299&_print=1 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) Fri Oct 10 07:53:56 PDT 2014 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=14017&_print=1 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? Best, Nancy Mon Sep 08 06:13:29 PDT 2014 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=10640&_print=1 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? Mon Apr 21 10:25:04 PDT 2014 https://skyline.ms/announcements/home/software/Skyline/tools/Support/QuaSAR/thread.view?rowId=9007&_print=1 Hi, 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. Luc Tue Feb 25 00:50:19 PST 2014