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bzhanglab / PepQuery

PepQuery: a targeted peptide search engine
http://pepquery.org
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Understanding sample names in Colon Prospective PNNL Proteome dataset #22

Closed VladimirRoudko closed 4 years ago

VladimirRoudko commented 4 years ago

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

wenbostar commented 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/.

wenbostar commented 4 years ago

Please reopen this issue if you still have any questions.

VladimirRoudko commented 4 years ago

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.

GuidoLeoni commented 3 years ago

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