A table to keep up with the conversion status in Toppas v2.1, KNIME and Galaxy. Status in the Conversion columns may be either empty (not started), WIP by XXX (work in progress by whom?), completed by XXX (conversion completed, but no test data run) or tested by XXX (test results are equal to TOPPAS results).
Please keep the file up to date as far as it concerns other team members, so we can avoid redundant work. Thanks a lot!
| WF | Test data (with location on server) | Conversion v2.1 | Conversion KNIME | Conversion Galaxy |
|---|---|---|---|---|
| GenerateShuffledDatabase_20150926 | D:\data\proteome-databases\uniprot-human-Nov26-2013-reference-reviewed-canonical-without-isoforms.fasta | tested @eppinglen | tested @eppinglen | |
| QualityControl_20151104 |
| WF | Test data with location on N: | Conversion v2.1 | Conversion KNIME | Conversion Galaxy |
|---|---|---|---|---|
| LabelFree_SciexTripleTOF_CentroidMode_20170111 | D:\data\Lars\20160121_LabelFree_SciexTripleTOF6600_Yasset\data\Yasset Perez-Riverol - 140702_0002_DC2ac_6600_G2_DDA1-DC2ac_6600_G2_DDA1.mzML,D:\data\proteome-databases-OpenMS\uniprot-koli-k12-nov24-2011-plus-shuffled.fasta | tested @eppinglen | tested @eppinglen | |
| PeptideQuantification_SciexTripleTOF6600_centroided_20170109 | D:\data\Lars\20160121_LabelFree_SciexTripleTOF6600_Yasset\data\Yasset Perez-Riverol - 140702_0002_DC2ac_6600_G2_DDA1-DC2ac_6600_G2_DDA1.mzML | tested @eppinglen | tested @eppinglen | |
| PeptideFeatureDetection_SciexTripleTOF6600_20170107 | D:\data\Lars\2015\20150709_FixedRatio_TripleTOF_Joern\data\SILAC_1_2000_3000.mzML | tested @eppinglen | tested @eppinglen | |
| SILACLys8Arg10_PeptideQuantification_SciexTripleTOF6600_20170107 | D:\data\Lars\2015\20150709_FixedRatio_TripleTOF_Joern\peptide_id\TOPPAS_out\004-PeakPickerHiRes-out\SILAC_2.mzML | tested @eppinglen | tested @eppinglen |
| WF | Test data with location on N: | Conversion v2.1 | Conversion KNIME | Conversion Galaxy |
|---|---|---|---|---|
| LabelFree_LTQOrbitrapXL_20170126 | D:/data/Lars/2015/20151111_BookChapterRSC/label_free/strepto_human_mix/data | tested @eppinglen | ||
| protein_quantification_Leu3SILAC_LTQOrbiXL_20160627 | N:/BM/BM40-48_Marius-Hefe | tested @eppinglen |
| WF | Test data with location on N: | Conversion v2.1 | Conversion KNIME | Conversion Galaxy |
|---|---|---|---|---|
| iTRAQ_LTQOrbitrapVelos_20151116 | D:\data\Lars\2015\20151111_BookChapterRSC\iTRAQ\PXD001265|tested @eppinglen | tested @eppinglen | ||
| QualityControl_20151106 |
| WF | Test data with location on N: | Conversion v2.1 | Conversion KNIME | Conversion Galaxy |
|---|---|---|---|---|
| LabelFree_QExactive_20151015 | N:\UK\UK181-209_Urinary_biomarkers_individual_samples_labelfree | tested @eppinglen | tested @eppinglen | |
| LabelFreeMultipleFractions_QExactive_20151016 | tested @eppinglen | new construction in Knime possible with group by loops | ||
| SILACArg6Lys6Labelling_QExactive_20151126 | N:/ST/ST895_908/ST897.mzML | tested @eppinglen | tested @eppinglen (diff:sp Q9NQP4 PFD4_HUMAN | |
| SILAC_Lys4Arg6_Lys8Arg10_QExactive20160627 | N:\UK\UK1_10_NMuMG_EMT_cathepsins_proteome_comparison_1| | |||
| DoubleDimethylLabelling_QExactive_20150707 | D:\data\Victor_Oginga\mass spec\data\analysis_Lars\results_precursor_correction\AGA116.mzML | tested @eppinglen | tested @eppinglen | |
| TripleDimethylLabelling_QExactive_20151115 | N:\CC\CC193-196\ D:\data\proteome-databases-OpenMS\uniprot-human-Nov26-2013-reference-reviewed-canonical-without-isoforms-plus-shuffled.fasta | tested @eppinglen | tested @eppinglen (diff: sp P25788 PSA3 HUMAN) | |
| TAILS_QExactive_20160609 | N:\WL\WL383_388\ | tested @eppinglen | workflow structure complete, different results (maybe FFM or MSGF+) | |
| TAILS_triple_QExactive_20161127 | N:\BM\BM2313_2324-necroptosis_uli-maurer_human-cells\ | tested @eppinglen | workflow structure complete, different results (maybe FFM or MSGF+) |