Closed VladimirRoudko closed 4 years ago
You can find the mapping information in this folder: https://cptc-xfer.uis.georgetown.edu/publicData/Phase_II_Data/S045_Colon_Cancer_Vasaikar2019/CPTAC_COprospective_metadata/.
Please reopen this issue if you still have any questions.
Ok, thank you!
On Apr 12, 2020, at 7:22 PM, Bo notifications@github.com wrote:
Please reopen this issue if you still have any questions.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bzhanglab/PepQuery/issues/22#issuecomment-612691164, or unsubscribe https://github.com/notifications/unsubscribe-auth/AESR5L65TVJB5J2GIVT35DDRMJEK3ANCNFSM4LXUSQXQ.
Hi Bo,
Sorry for the question which is an off-topic and directly not related to pepquery. I doing some peptide identifications in colon prospective PNNL dataset and would like to match my PSM to the actual patient ID - in order to correlate proteome to the genomics. I found it's hard to trace down the sample labels in PNNL dataset to the actual patient. For example, my search gave the following output:
SRQMESLGMK | TMT 10-plex of peptide N-term@0[229.1629];TMT 10-plex of K@10[229.1629] | 30 | 3 | 1,623.888 | -2.562 | 1,623.884 | 542.303 | 21.706 | 0 | 118 | 1 | 995 | 0.002008 | 1 | 0 | Retained | Yes | 09CPTAC_COprospective_W_PNNL_20170123_B3S1_f08:15737:3
however, "09CPTAC_COprospective_W_PNNL_20170123_B3S1_f08" does not match any patient id in supplemental data for Cell 2019 CPTAC paper or metadata stored on CPTAC server.
Thank you for your help,
Vladimir
Dear Vladimir did you managed how to solve this issue ? I'm performing a similar analysis on endometrial CPTAc dataset . By using the mapping info I'm able to identify all the samples in a TMT plex but I'm not able to understand how to associate a peptide to a specific patient Best regards Guido
Hi Bo,
Sorry for the question which is an off-topic and directly not related to pepquery. I doing some peptide identifications in colon prospective PNNL dataset and would like to match my PSM to the actual patient ID - in order to correlate proteome to the genomics. I found it's hard to trace down the sample labels in PNNL dataset to the actual patient. For example, my search gave the following output:
SRQMESLGMK | TMT 10-plex of peptide N-term@0[229.1629];TMT 10-plex of K@10[229.1629] | 30 | 3 | 1,623.888 | -2.562 | 1,623.884 | 542.303 | 21.706 | 0 | 118 | 1 | 995 | 0.002008 | 1 | 0 | Retained | Yes | 09CPTAC_COprospective_W_PNNL_20170123_B3S1_f08:15737:3
however, "09CPTAC_COprospective_W_PNNL_20170123_B3S1_f08" does not match any patient id in supplemental data for Cell 2019 CPTAC paper or metadata stored on CPTAC server.
Thank you for your help,
Vladimir