Package: sdrf-pipelines
sdrf-pipelinesThe SDRF pipelines provide a set of tools to validate and convert SDRF files to different workflow configuration files such as MSstats,OpenMS and MaxQuant.Installationpipinstallsdrf-pipelinesValidate the SDRFHow to use it:Then, you can use the tool by executing the following command:parse_sdrfvalidate-sdrf--sdrf_file{here_the_path_to_sdrf_file}Convert to OpenMS: Usageparse_sdrfconvert-openms-ssdrf.tsvDescription:experiment settings (search engine settings etc.)experimental designThe experimental settings file contains one row for every raw file. Columns contain relevevant parameters like precursor mass tolerance, modifications etc. These settings can usually be derived from the sdrf file.URIFilenameFixedModificationsVariableModificationsLabelPrecursorMassTolerancePrecursorMassToleranceUnitFragmentMassToleranceFragmentMassToleranceUnitDissociationMethodEnzymeftp://ftp.pride.ebi.ac.uk/pride/data/archive/XX/PXD324343/A0218_1A_R_FR01.rawA0218_1A_R_FR01.rawAcetyl (Protein N-term)Gln->pyro-glu (Q),Oxidation (M)label free sample10ppm10ppmHCDTrypsinftp://ftp.pride.ebi.ac.uk/pride/data/archive/XX/PXD324343/A0218_1A_R_FR02.rawA0218_1A_R_FR02.rawAcetyl (Protein N-term)Gln->pyro-glu (Q),Oxidation (M)label free sample10ppm10ppmHCDTrypsinThe experimental design file contains information how to unambiguously map a single quantitative value. Most entries can
be derived from the sdrf file. However, definition of conditions might need manual changes.Fraction_Groupidentifier that indicates which fractions belong together. In the case of label-free data, the fraction group identifier has the same cardinality as the sample identifier.TheFractionidentifier indicates which fraction was measured in this file. In the case of unfractionated data the fraction identifier is 1 for all samples.TheLabelidentifier. 1 for label-free, 1 and 2 for SILAC light/heavy, e.g. 1-10 for TMT10PlexTheSpectra_Filepath(e.g., path = "/data/SILAC_file.mzML")MSstats_Conditionthe condition identifier as used by MSstatsMSstats_BioReplicatean identifier to indicate replication. (MSstats requires that there are no duplicate entries. E.g., if MSstats_Condition, Fraction_Group group and Fraction number are the same - as in the case of biological or technical replication, one uses the MSstats_BioReplicate to make entries non-unique)Fraction_GroupFractionSpectra_FilepathLabelMSstats_ConditionMSstats_BioReplicate11A0218_1A_R_FR01.raw11112A0218_1A_R_FR02.raw111........115A0218_2A_FR15.raw11121A0218_2A_FR01.raw122................1015A0218_10A_FR15.raw11010For details, please see the MSstats documentationConvert to MaxQuant: Usageparse_sdrfconvert-maxquant-ssdrf.tsv-f{here_the_path_to_protein_database_file}-m{TrueorFalse}-pef{default0.01}-prf{default0.01}-t{temporaryfolder}-r{raw_data_folder}-n{numberofthreads:default1}-o1{parameters(.xml)outputfilepath}-o2{maxquantexperimentaldesign(.txt)outputfilepath}eg.parse_sdrfconvert-maxquant-s/root/ChengXin/Desktop/sdrf.tsv-f/root/ChengXin/MyProgram/search_spectra/AT/TAIR10_pep_20101214.fasta-r/root/ChengXin/MyProgram/virtuabox/share/raw_data/-o1/root/ChengXin/test.xml-o2/root/ChengXin/test_exp.xml-t/root/ChengXin/MyProgram/virtuabox/share/raw_data/-pef0.01-prf0.01-n4-s  : SDRF file-f : fasta file-r : spectra raw file folder-mcf : MaxQuant default configure path (if given, Can add new modifications)-m : via matching between runs to boosts number of identifications-pef : posterior error probability calculation based on target-decoy search-prf : protein score = product of peptide PEPs (one for each sequence)-t : place on SSD (if possible) for faster search，It is recommended not to be the same as the raw file directory-n : each thread needs at least 2 GB of RAM,number of threads should be ≤ number of logical cores available(otherwise, MaxQuant can crash)Descriptionmaxquant parameters file (mqpar.xml)maxquant experimental design file (.txt)The maxquant parameters file mqpar.xml contains the parameters required for maxquant operation.some settings can usually be derived from the sdrf file such as enzyme, fixed modification, variable modification, instrument, fraction and label etc.Set other parameters as default.The current version of maxquant supported by the script is 1.6.10.43Some parameters are listed：<fastaFilePath>TAIR10_pep_20101214.fasta</fastaFilePath><matchBetweenRuns>True</matchBetweenRuns><maxQuantVersion>1.6.10.43</maxQuantVersion><tempFolder>C:/Users/test</tempFolder><numThreads>2</numThreads><filePaths><string>C:\Users\search_spectra\AT\130402_08.raw</string><string>C:\Users\search_spectra\AT\130412_08.raw</string></filePaths><experiments><string>sample 1_Tr_1</string><string>sample 2_Tr_1</string></experiments><fractions><short>32767</short><short>32767</short></fractions><paramGroupIndices><int>0</int><int>1</int></paramGroupIndices><msInstrument>0</msInstrument><fixedModifications><string>Carbamidomethyl (C)</string></fixedModifications><enzymes><string>Trypsin</string></enzymes><variableModifications><string>Oxidation (M)</string><string>Phospho (Y)</string><string>Acetyl (Protein N-term)</string><string>Phospho (T)</string><string>Phospho (S)</string></variableModifications>For details, please see the MaxQuant documentationThe maxquant experimental design file contains name,Fraction,Experiement and PTM column.Most entries can be derived from the sdrf file.Nameraw data file name.FractionIn the Fraction column you must assign if the corresponding files shown in the left column belong to a fraction of a gel fraction. If your data is not obtained through gel-based pre-fractionation you must assign the same number(default 1) for all files in the column Fraction.ExperimentIn the column named as Experiment if you want to combine all experimental replicates as a single dataset to be analyzed by MaxQuant, you must enter the same identifier for the files which should be concatenated . However, if you want each individual file to be treated as a different experiment which you want to compare further you should assign different identifiers to each of the files as shown below.NameFractionExperimentPTM130402_08.raw1sample 1_Tr_1130412_08.raw1sample 2_Tr_1Convert to MSstats annotation file: Usageparse_sdrfconvert-msstats-s./testdata/PXD000288.sdrf.tsv-o./test1.csv-s  : SDRF file-c  : Create conditions from provided (e.g., factor) columns as used by MSstats-o  : annotation out file path-swath  : from openswathtomsstats output to msstats default false-mq  : from maxquant output to msstats default falseConvert to NormalyzerDE design file: Usageparse_sdrfconvert-normalyzerde-s./testdata/PXD000288.sdrf.tsv-o./testPXD000288_design.tsv-s  : SDRF file-c  : Create groups from provided (e.g., factor) columns as used by NormalyzerDE, for example-c ["characteristics[spiked compound]"](optional)-o  : NormalyzerDE design out file path-oc  : Out file path for comparisons towards first group (optional)-mq  : Path to MaxQuant experimental design file for mapping MQ sample names. (optional)CitationsDai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. PMID: 34615866; PMCID: PMC8494749.ManuscriptPerez-Riverol, Yasset, and European Bioinformatics Community for Mass Spectrometry. "Toward a Sample Metadata Standard in Public Proteomics Repositories." Journal of Proteome Research 19.10 (2020): 3906-3909.Manuscript