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MonashProteomics / FragPipe-Analyst

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DIA example needs to be adjusted #32

Closed hsiaoyi0504 closed 1 year ago

hsiaoyi0504 commented 1 year ago

Currently, the manifest of the DIA example (from ccRCC discovery cohort) is like this:

E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00010_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00183_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00103_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00088_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00004_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00183_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00004_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00096_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00097_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00026_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00026_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00096_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00103_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00010_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00079_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00079_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00088_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00011_NAT.mzML   NAT 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00011_T.mzML Tumor   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00097_NAT.mzML   NAT 1   DIA

But it should be

E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00010_T.mzML Tumor_1 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00183_NAT.mzML   NAT_1   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00103_NAT.mzML   NAT_2   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00088_NAT.mzML   NAT_3   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00004_T.mzML Tumor_2 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00183_T.mzML Tumor_3 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00004_NAT.mzML   NAT_4   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00096_T.mzML Tumor_4 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00097_T.mzML Tumor_5 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00026_NAT.mzML   NAT_5   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00026_T.mzML Tumor_6 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00096_NAT.mzML   NAT_6   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00103_T.mzML Tumor_7 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00010_NAT.mzML   NAT_7   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00079_NAT.mzML   NAT_8   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00079_T.mzML Tumor_8 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00088_T.mzML Tumor_9 1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00011_NAT.mzML   NAT_9   1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00011_T.mzML Tumor_10    1   DIA
E:\ccRCC_DIA\DIA_20files_mzML\CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00097_NAT.mzML   NAT_10  1   DIA

Therefore, the current DIA code needs to be changed.

hsiaoyi0504 commented 1 year ago

Compared to corresponding TMT data, DIA data relies on fp.manifest rather than a combined_annotation.txt. That means we don't have a condition column. Instead, we have a column called experiment.

Internal TMT DIA
replicate replicate bioreplicate
condition condition part of experiment cloumn (like Tumor in Tumor_1)
hsiaoyi0504 commented 1 year ago

Related to #15 and #20.

hsiaoyi0504 commented 1 year ago

fixed in https://github.com/MonashProteomics/Fragpipe-Analyst/commit/0527380626ce679bff8b8a2ca1a7d27b3b1f1448.