I exported from Mascot GUI a pepXML file and I tried to read it using the pepXMLTab R package:
library(pepXMLTab) options(stringsAsFactors=FALSE) pepXMLTab <- pepXMLTab::pepXML2tab(pepxml="F134048.xml")
but I got this error:
Error in (function (..., deparse.level = 1, make.row.names = TRUE, stringsAsFactors = default.stringsAsFactors(), : numbers of columns of arguments do not match
Do you have any idea of why this does not work? In principle my pepXML file should be a valid one since I was able to convert it to a .tsv using this tool: http://wlab.ethz.ch/tools/
Are there any compatibility issues between pepXMLTab and Mascot-generated pepXML files? Are there some options I had to set when exporting Mascot file to make it suitable to pepeXMLTab?
This is my sessionInfo():
R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 16299) Matrix products: default locale:  LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  pepXMLTab_1.18.0 loaded via a namespace (and not attached):  compiler_3.6.1 tools_3.6.1 XML_3.98-1.20*