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Rappsilber-Laboratory / XiSearch

XiSearch
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headers in *.ssl file #30

Closed ljavier2401 closed 5 years ago

ljavier2401 commented 5 years ago

Dear Prof. Rappsilber and colleagues, I wonder if in the *.ssl file to be uploaded by Skyline the headers describing the content for each column should remain inside the text file? Thank you in advance for you help. best regards, javier

lutzfischer commented 5 years ago

Short answer the header should stay.

Longer description: An example of a ssl file I just generated - that includes the header. Only the first few lines.

file    scan    charge  sequence    score-type  score
B170828_12_Lumos_ZC_IN_160_xHSA-1ug-3.mzML  33347   4   QNC[+57.021]ELFEQLGEYK[+1.008]FQNALLVRK[+25.968]QIK[+156.079]K[+1.008]QTALVELVK UNKNOWN 13.741058922881033
B170828_10_Lumos_ZC_IN_160_xHSA-1ug-1.mzML  17711   5   QIK[+155.095]K[+1.008]QTALVELVKK[+25.968]C[+57.021]C[+57.021]K[+1.008]ADDKETC[+57.021]FAEEGK    UNKNOWN 13.740688334198968
B170828_11_Lumos_ZC_IN_160_xHSA-1ug-2.mzML  27989   5   RHPYFYAPELLFFAK[+1.008]RK[+25.968]YK[+1.008]AAFTEC[+57.021]C[+57.021]QAADK[+155.095]AAC[+57.021]LLPK    UNKNOWN 13.727850250072883
B170828_11_Lumos_ZC_IN_160_xHSA-1ug-2.mzML  15216   4   D[+1.008]AHK[+155.095]SEVAHRK[+25.968]ADLAK[+1.008]YIC[+57.021]ENQDSISSK    UNKNOWN 13.622476521748698
B170828_11_Lumos_ZC_IN_160_xHSA-1ug-2.mzML  13698   4   LAK[+1.008]TYETTLEKK[+25.968]VTK[+1.008]C[+57.021]C[+57.021]TESLVNR UNKNOWN 13.62183158087037
B170828_10_Lumos_ZC_IN_160_xHSA-1ug-1.mzML  16560   4   D[+1.008]AHK[+156.079]SEVAHRK[+25.968]ADLAK[+1.008]YIC[+57.021]ENQDSISSK    UNKNOWN 13.584830418480474
B170828_11_Lumos_ZC_IN_160_xHSA-1ug-2.mzML  16975   4   K[+1.008]QTALVELVKK[+25.968]C[+57.021]C[+57.021]K[+1.008]ADDKETC[+57.021]FAEEGK[+156.079]K  UNKNOWN 13.564658135508324
B170828_10_Lumos_ZC_IN_160_xHSA-1ug-1.mzML  21270   4   FPK[+1.008]AEFAEVSKK[+25.968]LK[+1.008]EC[+57.021]C[+57.021]EK[+156.079]PLLEK   UNKNOWN 13.514157078721206
B170828_10_Lumos_ZC_IN_160_xHSA-1ug-1.mzML  20059   4   FPK[+1.008]AEFAEVSKK[+25.968]LK[+1.008]EC[+57.021]C[+57.021]EK[+155.095]PLLEK   UNKNOWN 13.504707177416872
B170828_10_Lumos_ZC_IN_160_xHSA-1ug-1.mzML  33308   5   LK[+155.095]C[+57.021]ASLQK[+1.008]FGERK[+25.968]MPC[+57.021]AEDYLSVVLNQLC[+57.021]VLHEK[+1.008]TPVSDR  UNKNOWN 13.495713858068333
B170828_11_Lumos_ZC_IN_160_xHSA-1ug-2.mzML  32549   5   QNC[+57.021]ELFEQLGEYK[+1.008]FQNALLVRK[+25.968]QIK[+1.008]K[+156.079]QTALVELVK UNKNOWN 13.386867744593532
B170828_11_Lumos_ZC_IN_160_xHSA-1ug-2.mzML  5906    4   ASSAK[+1.008]QRK[+25.968]VGSK[+1.008]C[+57.021]C[+57.021]K[+155.095]HPEAK   UNKNOWN 13.355664709269663

To make use of this you would need to define a set of modifications: The actual Modifications defined in xi: K[+155.09463] K[+156.07864] M[+15.99491] C[+57.02146] a modified lysine has inserted to represent the cross-linker mass: K[+25.968] In this example the actual cross-link sites is denoted by two separate modifications (helps distinguish peptide pairs with same peptides but distinct linkage sites): D[+1.00783] K[+1.00783]

These modifications need to be defined in skyline.

Ones these are defined you should be able to read in the library in skyline.

lutzfischer commented 5 years ago

Hi @ljavier2401 could you let me know if your question is sorted. Would like to close the issue

best regards, Lutz

On 30/01/2019 13:44, ljavier2401 wrote:

Dear Prof. Rappsilber and colleagues, I wonder if in the *.ssl file to be uploaded by Skyline the headers describing the content for each column should remain inside the text file? Thank you in advance for you help. best regards, javier

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ljavier2401 commented 5 years ago

Thank you very much for your answer and excuse me for my delay. Best regards, Javier

From: Lutz Fischer [mailto:notifications@github.com] Sent: Wednesday, February 13, 2019 11:13 AM To: Rappsilber-Laboratory/XiSearch Cc: Luis Javier Gonzalez; Mention Subject: Re: [Rappsilber-Laboratory/XiSearch] headers in *.ssl file (#30)

Hi @ljavier2401 could you let me know if your question is sorted. Would like to close the issue

best regards, Lutz

On 30/01/2019 13:44, ljavier2401 wrote:

Dear Prof. Rappsilber and colleagues, I wonder if in the *.ssl file to be uploaded by Skyline the headers describing the content for each column should remain inside the text file? Thank you in advance for you help. best regards, javier

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/XiSearch/issues/30, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGCYSE1FdPRDmfi8XqKIBdTKBL0elGAyks5vIZOvgaJpZM4aaIM6.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/XiSearch/issues/30#issuecomment-463260469, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AsTzz5WYQnlPb4ErbsEEpbfQtvwrgkjSks5vNDmNgaJpZM4aaIM6.