{"text_format":"3","workbook":"xlsx","n_sheets":3,"sheets":["Legend","A. Metrics from previous","B.Metrics used in this article"],"not_rendered":{"defined_names":2},"read":"whole","date_system":"1900"}

{"sheet":"Legend","index":0,"n_rows":1,"n_cols":1,"rows_kept":1}
["Supplementary Table 3. Selection and description of metrics. \nA. Metrics overview from previous articles. \nB. Metrics utilized in this article."]

{"sheet":"A. Metrics from previous","index":1,"n_rows":136,"n_cols":6,"rows_kept":136,"merged":[[133,12,134,12]]}
["Metric information","Location of Metrics","Metric specificity","Years","Journal Title","Article name"]
["Peptide Sequence Identified","Identifications: number of identified peptides or proteins","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["of precursors (1% FDR)","Identifications: number of identified peptides or proteins","DDA/DIA",2020,"Nature communication","Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies"]
["total number of identified peptides","Identifications: number of identified peptides or proteins","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Number of protein and peptides per condition","Identifications: number of identified peptides or proteins","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["total number of identified Proteins","Identifications: number of identified peptides or proteins","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["P-2C: Total peptide IDs (Unique tryptic peptides)","Identifications: number of identified peptides or proteins","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["IDs over RT","Identifications: peptide identification rates","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["C-2A: IQ RT period for IDs","Identifications: peptide identification rates","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["C-2B: IQ pep ID rate","Identifications: peptide identification rates","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Sequence coverage of proteins that match an entry in the proteins of interest list","Identifications: protein coverage","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["total number of identified PSMs ","Identifications: PSM","DDA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["P-2: Total peptide IDs (Unique spectra)","Identifications: PSM","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["P-3: Ratio of semi/full tryptic peptides","Identifications: ratio of semi/full tryptic peptides","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["P-1: Med.F-value score","Identifications: score","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Score","Identifications: score","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["Charge state distribution","Ion source: ionization efficiency","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["IS-2: precursor m/z","Ion source: ionization efficiency","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["IS-3A:Ratio of +1/+2 peptides","Ion source: ionization efficiency","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["IS-3B: Ratio of +3/+2 peptides","Ion source: ionization efficiency","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["IS-3C: Ratio of +4/+2 peptides","Ion source: ionization efficiency","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["IS-1A:10X intensity jumps","Ion source: ionization stability ","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["IS-1B:10X intensity fails","Ion source: ionization stability ","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Number of MS1 data points across LC peaks","LC: data point per peak","DDA/DIA",2020,"Nature communication","Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies"]
["MS2-2: Med.Num.Peaks","LC: number of peaks (seperation efficiency)","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Peak asymmetry of targeted peptides","LC: peak shape","DDA/DIA/SRM",2014,"J. Am. Soc. Mass. Spectrom","Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS"]
["C-1A: bleed -4min","LC: peak width (in a 4 minutes)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["C-1A bleed +4min","LC: peak width (in a 4 minutes)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Media LC peak width","LC: peak width (quartile)","DDA/DIA",2020,"Nature communication","Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies"]
["C-3A: Median peak widths","LC: peak width (quartile)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["C-3B: Peak with description","LC: peak width (quartile)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["C-4A: PW/half max, 1st decile","LC: peak width (quartile)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["C-4B: PW/half max, last decile","LC: peak width (quartile)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["C-4C: PW/half max, median","LC: peak width (quartile)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["FWHM of peptides","LC: peak width (targeted peptides)","DDA/DIA",2016,"Journal of proteome","An Automated Pipeline to Monitor System Performance in Liquid ChromatographyTandem Mass Spectrometry Proteomic Experiments"]
["full width at half maximum of targeted peptides","LC: peak width (targeted peptides)","DDA/DIA/SRM",2014,"J. Am. Soc. Mass. Spectrom","Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS"]
["peak width of definable peptides","LC: peak width (targeted peptides)","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Retention time (FWHM)","LC: peak width (targeted peptides)","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["Twins sequence fration (oversampling estimation)","LC: peptide overlappling (seperation efficiency)","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["C-6A: Fract. Extra early eluters","LC: retention time (in a period)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["C-6B: Fract. Extra late eluters","LC: retention time (in a period)","DDA/DIA/SRM",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Peptide elution time of definable peptides","LC: retention time (targeted peptides)","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["retention time of targeted peptides","LC: retention time (targeted peptides)","DDA/DIA/SRM",2014,"J. Am. Soc. Mass. Spectrom","Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS"]
["RT peak width distribution","LC: retention time distribution","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Peptide retention time","LC: retention time distribution","DDA/DIA",2016,"Journal of proteome","An Automated Pipeline to Monitor System Performance in Liquid ChromatographyTandem Mass Spectrometry Proteomic Experiments"]
["MBR alighment","Statistics: Parameters specific to Maxquant results","DDA/Maxquant",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["MRT RT matching","Statistics: Parameters specific to Maxquant results","DDA/Maxquant",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["General parameters seetings (Maxquant version, modification, ppm tol., FASTA datasbase, FDR cutoff, etc.)","Statistics: Parameters specific to Maxquant results","DDA/Maxquant",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Ratio of the transition peak area","MS1&MS2: ion fragmentation efficiecy ","DDA/DIA",2016,"Journal of proteome","An Automated Pipeline to Monitor System Performance in Liquid ChromatographyTandem Mass Spectrometry Proteomic Experiments"]
["MS1 ion injection time ","MS1: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS1 where maximum injection time was reched.","MS1: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Average MS1 total scan time","MS1: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS1 ion injection time ","MS1: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS1 scan time","MS1: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS2-4B: Fraction ID'd Q2 by intensity","MS2: acquisition efficiecy","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS2-4C: Fraction ID'd Q3 by intensity","MS3: acquisition efficiecy","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS2-4D: Fraction ID'd Q4 by intensity","MS4: acquisition efficiecy","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Mass precision ppm","MS1: MS accuracy","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["mass measurement accuracy","MS1: MS accuracy","DDA/DIA",2014,"J. Am. Soc. Mass. Spectrom","Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS"]
["Mass Error ppm","MS1: MS accuracy","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["MMA (Mass measuremeny accuracy)","MS1: MS accuracy","DDA/DIA",2016,"Journal of proteome","An Automated Pipeline to Monitor System Performance in Liquid ChromatographyTandem Mass Spectrometry Proteomic Experiments"]
["MS1 m/z deviation","MS1: MS accuracy","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["MS1 scan where lock-mass was detected","MS1: MS accuracy","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Average MS1 lock mass deviation","MS1: MS accuracy","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Lock mass detection and deviation","MS1: MS accuracy","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS1 decalibration","MS1: MS accuracy","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["MS1-5A: Median precursor-peptide m/z difference","MS1: MS accuracy (quartile)","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS1-5C: Median ppm precursor-peptide m/z difference","MS1: MS accuracy (quartile)","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS1-5D: Interquatile ppm precursor-peptide m/z difference","MS1: MS accuracy (quartile)","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Precursor peak area","MS1: peak area of targeted ions","DDA/DIA",2016,"Journal of proteome","An Automated Pipeline to Monitor System Performance in Liquid ChromatographyTandem Mass Spectrometry Proteomic Experiments"]
["DS-3A: MS max/sampled for IDs","MS1: sampling efficiency","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Number of MS1 scans","MS1: Scan number","DDA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["DS-2B: MS/MS scan over C-2A","MS1: scan number","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS1(%) of target value","MS1: signal","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS1-3A: 95th/5th MS1 maximum intensity","MS1: signal","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["DS-3B: MS1 max/sampled for bottom 50% by intensity","MS1: signal","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS1-3B: Median maximum intensity for IDs","MS1: signal","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS1-4A: MS1 signal varaition, within series","MS1: signal varation","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS1-4B: MS1 signal varaition, between series","MS1: signal varation","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS1 TIC","MS1: TIC signal","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS1-2B: Median TIC","MS1: TIC signal","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Ion injection time ","MS2: acquisition efficiecy ","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["MS/MS scans where maximum injection time was reached.","MS2: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Average MS/MS ion injection time ","MS2: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Average MS/MS total scan time","MS2: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS/MS ion injection time ","MS2: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS/MS scan time","MS2: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Cycle time","MS2: acquisition efficiecy ","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["MS1-1: Ion injection time for IDs","MS2: acquisition efficiecy ","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["m/z of triggered precursors","MS2: acquisition efficiecy ","DDA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["TopN over RT","MS2: acquisition efficiecy ","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["TopN","MS2: acquisition efficiecy ","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Identified by TopN","MS2: acquisition efficiecy ","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["MS2-1:Ion injection for IDs","MS2: acquisition efficiecy ","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS/MS (%) of target value","MS2: acquisition efficiecy ","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS/MS identified","MS2: acquisition efficiecy ","DDA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["MS2-4A: Fraction ID'd Q1 by intensity","MS2: acquisition efficiecy","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Total number of peaks in the spectrum","MS2: fragment ion variety","DDA/DIA",2018,"J. Am. Soc. Mass. Spectrom","Semi-supervised quality control method for proteome analyses based on tandem mass spectrometry"]
["MS/MS","MS2: MS accuracy","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["MS/MS scan where lock-mass was detected","MS2: MS accuracy","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["MS2 m/z deviation ","MS2: MS accuracy","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["MS2 fragment mass error","MS2: MS accuracy","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["MS1-5B: Median absolute precursors-peptide m/z difference","MS2: MS accuracy (quartile)","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["peak area of peptides","MS2: peak area of targeted ions","DDA/DIA",2016,"Journal of proteome","An Automated Pipeline to Monitor System Performance in Liquid ChromatographyTandem Mass Spectrometry Proteomic Experiments"]
["peak area of definable peptides","MS2: peak area of targeted ions","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Transition of peak area","MS2: peak area of targeted ions","DDA/DIA",2016,"Journal of proteome","An Automated Pipeline to Monitor System Performance in Liquid ChromatographyTandem Mass Spectrometry Proteomic Experiments"]
["Target peak area","MS2: peak area of targeted ions","DDA/DIA/SRM",2014,"J. Am. Soc. Mass. Spectrom","Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS"]
["Peptide intensity","MS2: peak area of targeted ions","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Intensity","MS2: peak area of targeted ions","DDA/DIA",2019,"Proteomics","QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems"]
["DS-1A: oversampling once/twice","MS2: sampling efficiency","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["DS-1B: oversampling twice/thrice","MS2: sampling efficiency","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["DS-2A: MS scans over C-2A","MS2: scan number","DDA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Number of MS/MS scans","MS2: scan number","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Average intensity","MS2: average signal","DDA/DIA",2018,"J. Am. Soc. Mass. Spectrom","Semi-supervised quality control method for proteome analyses based on tandem mass spectrometry"]
["MS2 TIC","MS2: TIC signal","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Apex intensity of definable peptides","Peptide quantitation","DDA/DIA",2012,"Journal of proteome","SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments"]
["Inter-injection median CV of precursors","Peptide quantitation","DDA/DIA",2020,"Nature communication","Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies"]
["SILIC only Ratio distribution","Peptide quantitation (SILAC related)","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["MS1-2A: S/N for IDs","Peptide quantitation: signal-to-noise","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["MS2-3:S/N for IDs","Peptide quantitation: signal-to-noise","DDA/DIA",2010,"Mol Cell Proteomics","Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses"]
["Protein Intensity (MS1, Itraq reporter, [LFQ])","Peptide quantitation: targeted peptides","DDA/DIA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["User-defined contaminants","Sample preparation: contamination","DDA/DIA/SRM",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Contaminants","Sample preparation: contamination","DDA/DIA/SRM",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Fraction of contaminats","Sample preparation: contamination","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Missed cleavage","Sample preparation: enzyme efficiency","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["Missed cleavage distribution","Sample preparation: enzyme efficiency","DDA",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["PCA plot","Statistical analysis ","DDA/DIA/SRM",2015,"Journal of proteome","Proteomics Quality Control: Quality Control Software for MaxQuant Results "]
["ID-free metrics from QuaMeter","Statistical analysis ","Statistical analysis ",2016,"Journal of proteome","Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics"]
["Features from QueMeter and NEST","Statistical analysis ","Statistical analysis ",2013,"Journal of proteome","Signatures of Mass Spectrometry Data Quality"]
["ID-free metrics from QuaMeter","Statistical analysis ","Statistical analysis ",2016,"Journal of proteome","Unsupervised Quality Asseaasment of Mass spectrometry Proteomics Experiment by Multivariate Quality Control Metrics"]
["Correlation coefficient","Statistical analysis ","Statistical analysis ",2011,"Bioinformatics","Improved quality control processing of peptide-centric LC-MS proteomics data "]
["reaction of missing peptide abundance data","Statistical analysis ","Statistical analysis ",2011,"Bioinformatics","Improved quality control processing of peptide-centric LC-MS proteomics data "]
["median absolute deviation of peptides within a LC-MS run","Statistical analysis ","Statistical analysis ",2011,"Bioinformatics","Improved quality control processing of peptide-centric LC-MS proteomics data "]
["The asymmetry of a distribution is described by skew","Statistical analysis ","Statistical analysis ",2011,"Bioinformatics","Improved quality control processing of peptide-centric LC-MS proteomics data "]
["kurtosis","Statistical analysis ","Statistical analysis ",2011,"Bioinformatics","Improved quality control processing of peptide-centric LC-MS proteomics data "]
["Missingness","Statistical analysis ","Statistical analysis ",2011,"Bioinformatics","Improved quality control processing of peptide-centric LC-MS proteomics data "]

{"sheet":"B.Metrics used in this article","index":2,"n_rows":16,"n_cols":5,"rows_kept":16}
["Metric ID","Metrics information","Location of metrics","Resource","Metrics specificity"]
["F1","Peak width (FWHM) of targeted peptide precursors","Chromatography","DIA-NN results","DIA/SWATH/diaPASEF"]
["F2","Retention time of targeted peptide precursors","Chromatography","DIA-NN results","DIA/SWATH/diaPASEF"]
["F3","Precursor ion chromatogram","Chromatography","mzXML","DIA/SWATH/diaPASEF"]
["F4","Charge state distribution","Ion source","DIA-NN results","DIA/SWATH/diaPASEF"]
["F5","Intensity variation of adjacent MS1 scan","Ion source","mzXML","DIA/SWATH/diaPASEF"]
["F6","Precursor mass accuracy","MS1 scan","DIA-NN results","DIA/SWATH/diaPASEF"]
["F7","TIC MS1 signal","MS1 scan","DIA-NN results","DIA/SWATH/diaPASEF"]
["F8","Fragment mass accuracy","MS2 scan","DIA-NN results","DIA/SWATH/diaPASEF"]
["F9","TIC MS2 signal","MS2 scan","DIA-NN results","DIA/SWATH/diaPASEF"]
["F10","Ratio of peak area of MS1 to MS2 signal","MS2 scan","DIA-NN results","DIA/SWATH/diaPASEF"]
["F11","Number of identified peptides","Identification and quantitation","DIA-NN results","DIA/SWATH/diaPASEF"]
["F12","Number of identified protiens","Identification and quantitation","DIA-NN results","DIA/SWATH/diaPASEF"]
["F13","MS1 area of targeted peptide precursors","Identification and quantitation","DIA-NN results","DIA/SWATH/diaPASEF"]
["F14","MS2 intensity of targeted peptide precursors","Identification and quantitation","mzXML","DIA/SWATH/diaPASEF"]
["F15","Ion mobility accuracy","MS1 scan","mzXML","diaPASEF"]