diff --git a/docs/README.adoc b/docs/README.adoc index 2b062ee..b6e0e9a 100644 --- a/docs/README.adoc +++ b/docs/README.adoc @@ -195,7 +195,7 @@ A Parquet table can be distributed across multiple compute nodes, and its key ad [cols="6*", options="header"] |=========================================================================================== -| Project | Type | File size(GB) | Convert size(MB) | Psm time(s) | Feature time(s) +| Project | Type | Original file size(GB) | Converted parquet size(MB) | Writing psm time(s) | Writing feature time(s) | PXD046440 | maxquant | 48 | 337/343 | 985.2671835 | 678.474133 | PXD016999 | mzTab | 160 | 155/228 | 539.0019641 | 3554.52738 | PXD019909 | diaNN | 1.9 | 195 | | 229.482332 diff --git a/docs/field_msg.tsv b/docs/field_msg.tsv new file mode 100644 index 0000000..e7708c2 --- /dev/null +++ b/docs/field_msg.tsv @@ -0,0 +1,35 @@ +field ontology_name ontology_accession desc +sequence +peptidoform peptidoform MS:1003049 "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." +modifications +precursor_charge +posterior_error_probability posterior error probability from identification based on multiple spectra MS:1003336 PEP score for identifications based on multiple spectra. +is_decoy +calculated_mz +observed_mz +mp_accessions +predicted_rt predicted retention time MS:1000897 A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application. +reference_file_name +scan scan number MS:1003057 Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run. +rt retention time MS:1000894 A time interval from the start of chromatography when an analyte exits a chromatographic column. +ion_mobility ion mobility drift time MS:1002476 Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated. +number_peaks number of peaks MS_1003059 "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." +mz_array m/z array MS_1000514 A data array of m/z values. +intensity_array intensity array MS:1000515 A data array of intensity values. +anchor_protein anchor protein MS:1001591 A representative protein selected from a set of sequence same-set or spectrum same-set proteins. +unique peptide unique to one protein MS:1001363 A peptide matching only one. +pg_global_qvalue protein-level global FDR MS:1001214 Estimation of the global false discovery rate of proteins. +start_ion_mobility +stop_ion_mobility +gg_accessions "Gene accessions, as string array" +gg_names "Gene names, as string array" +rt_start +rt_stop +andromeda_score Andromeda:score MS:1002338 The probability based score of the Andromeda search engine. +andromeda_delta_score Andromeda: delta score MS:1003433 +percolator_score percolator:score MS:1001492 Percolator:score. +openms_score OpenMS:Best PSM Score MS:1003114 The score of the best PSM selected by the underlying identification tool +msgf_score MS-GF:RawScore MS:1002049 MS-GF raw score. +consesus_support +parent_ion_score Short for Parent Ion Fraction; indicates the fraction the target peak makes up of the total intensity in the inclusion window. +quantitative_score "when using QuantUMS is equal to 1.0 / (1.0 + SD), where SD is the standard deviation of the LC-MS-derived error in relative precursor quantification" diff --git a/docs/score_map_msg.tsv b/docs/score_map_msg.tsv deleted file mode 100644 index 17e7257..0000000 --- a/docs/score_map_msg.tsv +++ /dev/null @@ -1,7 +0,0 @@ -field ontology_name ontology_accession -andromeda_score Andromeda:score MS:1002338 -andromeda_delta_score Andromeda: delta score MS:1003433 -percolator_score percolator:score MS:1001492 -openms_score OpenMS:Best PSM Score MS:1003114 -msgf_score MS-GF:RawScore MS:1002049 -posterior_error_probability posterior error probability from identification based on multiple spectra MS:1003336