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Open MS Workflow Conversion Status

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!

Misc

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

Sciex, TripleTOF 6600

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

Thermo, LTQ Orbitrap XL

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

Thermo, Orbitrap Velos

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

Thermo, Q Exactive

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+)