Hi Brian, Jimmy, David, Thanks for all the suggestions!
I did all you suggested: generated .mgf file, re-searched by Mascot, renamed .dat file......., and they all worked for the file I have been trying (SSM411, as Jimmy pointed out) so far. But, when I tried the different mzXML files (since SSM411 is just one of the fractions), I was stuck on Mascot searching. I have tried another 4 different mzXML files, they all gave me similar error massages: Max number of ions is 10000. Ignoring ms-ms set starting at line 139813 [M00031] Your search is continuing... Warning: .............................(similar warnings with different line numbers) ....................... ....................... Max number of ions is 10000. Ignoring ms-ms set starting at line 154038 [M00031] Your search is continuing... Warning: Your search is continuing... Sorry, your search could not be performed due to the following mistake entering data. Missing ion intensity value on line 3857088 of input file [M00430] Please press the back button on your browser, correct the fault and retry the search. Another problem is although the SSM411.mgf file worked on Mascot search, the results is a bit different from what I got earlier searched by pkl files generated by PLGS (Waters). The result from .mgf (converted by MzXML2Search) gives 33 identified proteins, and the one from .pkl (converted by PLGS) gives 39 identified proteins. The result from .mgf also gives fewer number of "peptide matches above identity threshold" compared to result from .pkl file (104 vs. 135). I also tried to generate .pkl file by MzXML2Search command just for the curiosities. It gives the very similar result compared to the search from .mgf file. The only differece is ""peptide matches above identity threshold" with 103 instead of 104. The search from .pkl file (converted by PLGS) didn't give any warning message during the searching process, while the .mgf and .pkl (converted by MzXML2Search) gave the similar warning message as follows: Max number of ions is 10000. Ignoring ms-ms set starting at line 275395 [M00031] Your search is continuing... ....................... (similar warnings with different line numbers) ....................... Your search is continuing... Finished uploading search details and file... Searching.... Warning: Error 31 has been detected 26 times and only the first 10 messages have been output [M00999] Your search is continuing... .20% complete ..50% complete Any suggestions for fixing? Thanks in advance, Jing -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
