System cannot find the specified file?!

[jaimejj]

Hi.

(a) I am trying to run a pepchem converted t2d file from MALDI ToF/ToF 5800 in search gui. But the search gets cancelled every time after the file conversion. Pls see the attached file. error file.txt What should I do?

(b) I am interested to perform an error tolerant search as in Mascot search engine. I am rather new to this software. Kindly advise on what I should use/do.

Thanks. j

[hbarsnes]

Hi J,

(a) I am trying to run a pepchem converted t2d file from MALDI ToF/ToF 5800 in search gui. But the search gets cancelled every time after the file conversion.

It seems like the conversion of the td2 files to mgf does not work. I would recommend trying to convert the raw files separately in ProteoWizard (http://proteowizard.sourceforge.net) and then use the resulting mgf files as input in SearchGUI. If there is still a problem converting the raw files I recommend contacting the ProteoWizard team directly.

(b) I am interested to perform an error tolerant search as in Mascot search engine. I am rather new to this software. Kindly advise on what I should use/do

At the moment none of the search engines included in SearchGUI support these type of searches. We are however working on adding support for MetaMorpheus, which should support some of the features included in Mascot's error tolerant search.

May I ask which aspects of the error tolerant search you are most interested in? As some of them may already be covered under different names for the search engines already supported in SearchGUI.

Best regards, Harald

[jaimejj]

Hi Harald,

Thank you for your prompt reply.

Converting the raw files separately in ProteoWizard ( http://proteowizard.sourceforge.net) appeared to work, but for some reason still not able to use these files as input in SearchGUI. Sure, I will be in touch with the support team.

With regards to error tolerant search, I am interested in amino acid substitution (Peptide sequence not in the database). If possible,I would like to test all possible amino acid substitutions for my protein.

Any advice?

Thanks, j

On Mon, 7 Sep 2020 at 19:16, Harald Barsnes notifications@github.com wrote:

Hi J,

(a) I am trying to run a pepchem converted t2d file from MALDI ToF/ToF 5800 in search gui. But the search gets cancelled every time after the file conversion.

It seems like the conversion of the td2 files to mgf does not work. I would recommend trying to convert the raw files separately in ProteoWizard ( http://proteowizard.sourceforge.net) and then use the resulting mgf files as input in SearchGUI. If there is still a problem converting the raw files I recommend contacting the ProteoWizard team directly.

(b) I am interested to perform an error tolerant search as in Mascot search engine. I am rather new to this software. Kindly advise on what I should use/do

At the moment none of the search engines included in SearchGUI support these type of searches. We are however working on adding support for MetaMorpheus, which should support some of the features included in Mascot's error tolerant search.

May I ask which aspects of the error tolerant search you are most interested in? As some of them may already be covered under different names for the search engines already supported in SearchGUI.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/searchgui/issues/250#issuecomment-688257902, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPRJ2QT3KHIAT6YJ6KZ4P3SES6JTANCNFSM4Q5K7JEQ .

-- " PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya

("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang

termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut.

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[hbarsnes]

Hi J,

With regards to error tolerant search, I am interested in amino acid substitution (Peptide sequence not in the database). If possible, I would like to test all possible amino acid substitutions for my protein.

I'm afraid this is not currently supported by the search engines in SearchGUI, but it should be possible as soon as we get to release a version that also includes MetaMorpheus.

Best regards, Harald

[hbarsnes]

Issue assumed resolved. If this is not the case, please let us know and we'll reopen the issue.

Also note that the new version of SearchGUI that has just been released now includes MetaMorpheus which should allow you to search for the amino acid substitutions.

[jaimejj]

Hi Harald.

Thank you for the update on metamorpheus. Really appreciate it.

Good day!

jaime

On Wed, 4 Nov 2020 at 22:56, Harald Barsnes notifications@github.com wrote:

Issue assumed resolved. If this is not the case, please let us know and we'll reopen the issue.

Also note that the new version of SearchGUI that has just been released now includes MetaMorpheus which should allow you to search for the amino acid substitutions.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/searchgui/issues/250#issuecomment-721780389, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPRJ2QQVXUIAZTWFJ2COCLSOFTRZANCNFSM4Q5K7JEQ .

-- " PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang

termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut.

DISCLAIMER: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of University of Malaya shall be understood as neither given nor endorsed by any of the forementioned. "