Fragment ion intensities

[GolAGitHub]

Hello,

I would like to extract fragment ion intensities following a search of DIA data. How can I map the ";"-separated values from the column "Fragment.Quant.Raw" in the report to the "FragmentType" / "FragmentCharge" / "FragmentSeriesNumber" specified in report-lib?

Thank you!

[vdemichev]

Hi, please add --report-lib-info to 'Additional options', the main report will then contain fragment annotation.

[GolAGitHub]

Thank you!

[GolAGitHub]

Hello there! Following my recent inquiry, I was able to retrieve fragmentation annotations. However, looking at the information retrieved, I noticed that in a few instances, the annotations contained duplicated ions. Here is an example: y8^2/441.740448;y8^1/882.4730835;y6^1/714.3831787;y7^1/785.4202881;y5^1/551.3198853;y3^1/393.2507324;y4^1/464.2878418;y9^2/498.2824707;b3^1/340.1872559;y7^1/393.2140503;y6^2/357.6954956;b6^1/661.3197021; y7^1 appears twice. I simply seems that the second occurrence should be y7^2 Although the m/z values after the “\” are correct (714.3831787 for the first 393.2140503 for the second), this could potentially cause some issues for those (like me) relying exclusively on the identity of the ion, and should probably be corrected in the future. I’ll be happy to provide additional information if needed. Kind regards. Guillaume From: Vadim Demichev ***@***.***> Sent: Wednesday, July 06, 2022 6:12 AM To: vdemichev/DiaNN ***@***.***> Cc: Adelmant, Guillaume O. ***@***.***>; Author ***@***.***> Subject: Re: [vdemichev/DiaNN] Fragment ion intensities (Discussion #425) External Email - Use Caution Hi, please add --report-lib-info to 'Additional options', the main report will then contain fragment annotation. — Reply to this email directly, view it on GitHub<https://secure-web.cisco.com/1o_P8_Jg94C1_Lf2hZPf0gGs1rY1YtOpGBx0LVZwpfGrKzBOJ1ME9NZ9GJEEkQtIR1MoooYSq5EkP9c-tpw9_SpmIa2OsYebrcXYjEccsmO1TusemrYEgJzx0UsrM3xGrTt_dXWmMamwjRx3DXD9m6j3oFB3inT6pT6jMBIIFnNqTZmgfLQx87TqSIJx1tLTghwzbTIiHTUHRXfnI-xBZ8siMxJvwA0akLjC6sZbAnpDd1H-WyPuGQJmTHOnqsUQ5jW7kvqkECnOS1Zgx_LMREhmTP1-_f6vYwskAmWuZUy5resbX8sdSXLHWuLi9hgsa2OuXa_-ZvpvkKjOZbV-W3w/https%3A%2F%2Fgithub.com%2Fvdemichev%2FDiaNN%2Fdiscussions%2F425%23discussioncomment-3091223>, or unsubscribe<https://secure-web.cisco.com/1ZTCQ90iDYaccdwTuex-CpH5APyyKLlpX25AQhX2mifvwMTW0M0RQBO6EsBSa1cNWaCPzXfZU_4qHluAXn59jG_-Ku07tOZMVWJobLiq_oZf9tBrjzsaBpl6VwOoxAbxe0gtMs-clffaKNm904S9yc9PB9yxkqOBO6iJMF7O0432mEwdrXmQ3jqyrU_nwgp6q8EM2vss6ewLnB86UNLr4UTmqHLynT176d0BOhSxqyZhvyQWe7yJxH0b9iVWtGs75tGWNtfowBjA83xclp_gkbcJ-L16f2-P3bhUpV1OMDOUB1qRK9MqB9rGkaJOoGQ_6O99jKJH1QSBBA4ePdfVJAw/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAZ5JJH7JC7MEAKFF75QYV6TVSVLX3ANCNFSM52UFG4AQ>. You are receiving this because you authored the thread.Message ID: ***@***.***> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

[vdemichev]

Hi Guillaume

How are the respective fragments annotated in the spectral library you are using?

Best,
Vadim

[GolAGitHub]

Hi Vadim, The library was created by DIANN directly. I presume these are the spectral library files: report-lib.tsv.speclib report-lib.predicted.speclib If these are the correct files, what application should I use to open them? Thank you! Guillaume From: Vadim Demichev ***@***.***> Sent: Saturday, July 30, 2022 3:02 AM To: vdemichev/DiaNN ***@***.***> Cc: Adelmant, Guillaume O. ***@***.***>; Author ***@***.***> Subject: Re: [vdemichev/DiaNN] Fragment ion intensities (Discussion #425) External Email - Use Caution Hi Guillaume How are the respective fragments annotated in the spectral library you are using? Best, Vadim — Reply to this email directly, view it on GitHub<https://secure-web.cisco.com/12cegkK7JqJP7GtHCvKbrzEiMg-QIErejiEjhSN_x8ARmcbluMydZ5MZZMTa6S2wZDrJkCWxru3DtY4O4H_kAijwc8nT0PlPUp5qDL_qdsD2xFvfWyZWnLvMEajtmKSf53CoHr1-yu-rSgV0-AYY8Q85CJKyYBwYdnC5Qi8IzVuBzKsz-NPQyC0Kjs5IoK29wjD96hHk6lqPwdnTfOHeMUsSHOJjjrx9NGcHllIJgruL7BoiLmM_yDIB-EfuEu2fNpb53JTXDMYiFfIQyEPv0zNn9w8oiIuFI3wXeD-rcUvPIFNOu5ZUwZ3jXYXKp7YGf-hnuREoy3gsNuuimQYbITw/https%3A%2F%2Fgithub.com%2Fvdemichev%2FDiaNN%2Fdiscussions%2F425%23discussioncomment-3285735>, or unsubscribe<https://secure-web.cisco.com/1ndsxNBU7SPmXiJKci6vBukpTfqYCaQnGTNMk-DMDVHdjVto64G15tIQshJ7Nd8nCbfJoqyvsU4Fecrey39Xmw-S6bTyAh9SAL3aHI7fXeoG2HUynJc4ve9IQ-U2hyFNYPly0PvymPFpQi4AbB-XJbpBYeWmD4TObImou1I_aoFgNgYGGiZMC2FOTRvzIet9WQVvw5L9BHtMV8Ij4iBqxXwVZSWGqVfXZ_bFqf0RttkjVRtvxxMvirtGkHkV551CyNYL2gd2Mr-IJO_3N4vJDI7WsV5YETB__PLCdjyDYsya0sBBBtJi4c0RLOO0q5hqs2oXiiK4jCqt6qqm8Ki5RJg/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAZ5JJH2Z4UXIWILV22IF3OLVWTHM3ANCNFSM52UFG4AQ>. You are receiving this because you authored the thread.Message ID: ***@***.***> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

[vdemichev]

Any .speclib file can be converted using DIA-NN to .tsv, so the respective .tsv lib can be examined using R/Python