HUPO Proteomics Standards Initiative Abbreviations
From Mass Spec Terms
version 4.1.22, Jan 25, 2019; https://github.com/HUPO-PSI/psi-ms-CV
List of MS-related abbreviations: ================================= * ABRF Association of Biomolecular Resource Facilities * ABSI Atomic Beam Surface Ionization * ABSI Appearance Energy * ADE Amide Dead End * AGHIS All-Glass Heated Inlet System * AIF All Ion Fragmentation * AIMS Accurate Inclusion Mass Screening * AMEx Accurate Mass Exclusion * AMS Accelerator Mass Spectrometry * AMT Accurate Mass and Retention Time; Accurate Mass Tag * ANDI ANalytical Data Interchange protocol * ASAP-Ratio Automated Statistical Analysis of Protein Ratio * ASMS American Society for Mass Spectrometry * APEX Absolute Protein Expression Index * APCI Atmospheric Pressure Chemical Ionization * API Atmospheric Pressure Ionization * APPI Atmospheric Pressure Photo-Ionization * APS Active Pixel Sensor * ASAPRatio Automated Statistical Analysis of Protein Abundance Ratio * ASMS American Society for Mass Spectrometry * ATAQS Automated and Targeted Analysis with Quantitative SRM * AQUA Absolute QUAntification (of proteins) * BDRG Biotin-Aspartate-Rink-Glycine * BFP Blue Flourescent Protein * BIRD Blackbody Infrared Radiative Dissociation * BONCAT BioOrthogonal Non-Canonical Amino acid Tagging * BPC Base Peak Chromatogram * BPI Base Peak Intensity chromatogram * ChEBI CHemical Entities of Biological Interest * CA Collisional Activation * CAD Collisionally Activated Dissociation * CAI Codon Adaption Index * CAM CarbAmidoMethyl * CCS Collision Cross-Section * CDA Chemical Detector Array * CDIT Culture Derived Isotope Tag * CD Cytoplasmic Domain (immunology) * CE-CI Charge Exchange Chemical Ionization * CEI Charge Exchange Ionization * CEM Channel Electron Multiplier * CEMA Channel Electron Multiplier Array * CF-FAB Continuous-Flow Fast Atom Bombardment * CHOPIN CHarge Ordered Parallel Ion aNalysis * CI Chemical ionization * CID Collision Induced Dissociation * CIT Caltech Isobaric Tags * CLIP Click-enabled Linker for Interacting Proteins * CNL Constant Neutral Loss * CODACON CODed Anode Converter * COFRADIC COmbined FRActional DIagonal Chromatography * CPAS Computational Proteomics Analysis System * CPTAC Clinical Proteomic Tumor Analysis Consortium * CPM Continuous Profile Mode * CPP Cell Penetrating Peptides * cps counts per second * CRC Collision Reaction Cell * CRD Charged-Residue Model * CRF Charge Remote Fragmentation * CRM Certified reference Material / Charged-Residue Model / Consecutive Reaction Monitoring * CSR Charge Stripping Reaction * CTIA Charge-TransImpediance Amplifier * CXL Cliackable Cross-Linker * CZE Capillary Zone Electrophoresis * dNSAF distributed Normalized Spectral Abundance Factor * DADI Directed Analysis of Daughter Ions * DAPCI Desorption Atmospheric Pressure Chemical Ionization * DART Direct Analysis in Real Time * DCI Desorption Chemical Ionization * DDA Data Dependent Analysis * DDDT Data Dependent Decision Tree (CAD, ETD) * DE Delayed Extraction * DEI Direct Electron Ionization * DEP Direct Exposure Probe * DESI Desorption ElectroSpray Ionization * DGMS Deutsche Gesellschaft fr MassenSpektrometrie * DiART Deuterium isobaric Amine Reactive Tag) * DiLeu Dimethyl Leucine * DIA Data Independent Acquisition * DIMS Direct Infusion Mass Spectrometry * DIOS Desorption Ionization On Silicon * DIP Direct Insertion Probe * DIGE DIfference Gel Electrophoresis * DIT Digital Ion Trap * DLI Direct Liquid Introduction * DMEM Dulbeccos Modified Eagle Medium * DMS Differential Mobility Spectrometry * DSIMS Dynamic Secondary Ion Mass Spectrometry * DTA Differential Thermal Analysis * EASI Easy Sonic Spray Ionization * ECAT Element-Coded Affinity Tag * ECD Electron Capture Dissociation * EDD Electron Detachment Dissociation * EDE Ester Dead End * EESI Extractive ElectroSpray Ionization * EI Electron Ionization (also known as Electron Impact Ionization) * EIC Extracted Ion Current * ELDI Electrospray-Assisted Laser Desorption / Ionization * EM Electron Multiplier * EMA European Medicines Agency * emPAI exponentially modified Protein Abundance Index (10^PAI - 1) * EOID Electro-Optical Imaging Detector * ERAD Endoplasmatic reticulum-Associated protein Degradation * ERLIC Electrostatic Repulsion hydrophiLic Interaction Chromatography * ERPA Extended Range Proteomic Analysis * ESI ElectroSpray Ionization * EST Expressed Sequence Tag * ETD Electron Transfer Dissociation * ETCaD Electron-Transfer Collisionally-activated Dissociation * EThcD Electron-Transfer/Higher-energy Collision Dissociation * FAB Fast Atom Bombardment * FACS Fluorescence Activated Cell Sorting * FAIMS Field Asymmetric Ion Mobility Spectrometry * FASP Filter-Aided Sample Preparation * FDR False Discovery Rate * Fe-IMAC Iron-Immobilized Metal ion Affinity Chromatography * FFPE Formalin-Fixed Paraffin Embedded * FFR Field Free Region * FID Flame Ionization Detector * FLR False Localization Rate * FNR False Negative Rate * FPC Focal Plane Camera * FPKM Fragments Per Kilobase of transcript per Million mapped reads * FPR False Positive Rate * FT-ICR Fourier Transform Ion Cyclotron Resonance * FTMS Fourier Transform Mass Spectropmetry * FuGE Functional Genomics Experiment * FWER Family-Wise Error Rate * FWHM Full Width at Half Maximum * GFP Green Flourescent Protein * HCD High-energy Collision-induced Dissociation; High-energy C-trap Dissociation * HCT High Capacity ion Trap * HDMS<sup>E</sup> MS<sup>E</sup> combined with mobility separation * HILIC Hydrophilic interaction Chromatography * H-PINS Halogenated-Peptides as INternal Standards * HPLC High Performance (Pressure) Liquid Chromatography * HRM Hyper Reaction Monitoring * HRAM High-Resolution Accurate Mass * HSA Human Serum Albumin * iARTS isobaric Aldehyde Reactive Tags * iBAC Intensity Based Absolute Quantification * ICAT Isotope Coded Affinity Tag * ICATXL Isotope-Coded and Affinity-Tagged Cross-Linking * ICC Immuno-Competitive Capture * ICCL Isotopically-Coded Cross-Linker * ICD Isotope Coded Derivatization * ICNTM Isotopically-Coded N-Terminal Modification * ICR Ion Cyclotron Resonance * ICP Inductively Coupled Plasma * ICPL Isotope Coded Protein Label(ing) * IDA Isotope Dilution Analysis * IDMS Isotope Dilution Mass Spectrometry * IEF IsoElectric Focusing * IEM Ion Evaporation Model * IEX Ion EXchange chormatography * IML Identical Mass Linker * IMAC Immobilized Metal Affinity Chromatography * IMS Imaging Mass Spectrometry / Ion Mobility Spectrometry * IRMPD InfraRed Multi-Photon Dissociation * ISD In Source Decay * ITA Ion Trap Array * ITMS Ion Trap Mass Spectrometry * iTRAQ isobaric tags for Relative and Absolute Quantification * iTRAQH isobaric tags for Relative and Absolute Quantification Hydrazide * IPD Isotope Pattern Deconvolution * IPI International Protein Index * iPRG Proteome Informatics research Group * IPTL Isobaric Peptide Termini Labeling * IRMPD InfraRed MultiPhoton Dissociation * IRMS Isotope Ratio Mass Spectrometry * iTRAQ isobaric Tag for Relative and Absolute Quantitation * LAESI Laser Ablation ElectroSpray Ionization * LCC Liquid Chromatography Combustion * LCD Laser Capture Microdissection * LFQ Label Free Quantification * LID Laser Induced Dissociation * LIFDI Liquid Injection Field Desorption * LIFT Linear Flight Time / Linear Inverse Fourier Transform ? * LIMS Laboratory Information Management System * LiP Limited Proteolysis * LIT Linear Ion Trap * LLOQ Lower Limit Of Quantification * LOB Limit Of Blank * LOD Limit Of Detection * LOQ Limit Of Quantification * LTQ Linear Trap Quadrupole * MAAH Microwave-Assisted Acid Hydrolysis * MALDI Matrix Assisted Laser Desorption and Ionisation * MATI Mass-Analyzed Threshold Ionization * MBSI Molecular Beam Surface Ionization * MCL Maximum Contaminant Level * MCP Micro Channel Plate * MCCP Multi-Classifier Combinatorial Proteomics * MDL Mass Defect Labeling * MeCAT Metal-Coded Affinity Tag * MELDI Material Enhanced Laser Desorption Ionization * MFCA Micromachined Faraday Cup Array * MIAPE Minimum Information about A Proteomics Experiment * MIC Multi Ion Counting * MIDAS Modular Ion cyclotron resonance Data Acquisition System * MIDAS (MR)Monitoring-Initiated Detection And Sequencing * MIKES Mass-analyzed Ion Kinetic Energy Spectrometry * MIPA MInimally Permutated Analogs * MMTS Methyl-MethaneThioSulfonate * MOWSE MOlecular Weight SEarch * MPD Multi Photon Dissociation * MPF Mobile Proton Factor * MRM Multiple Reaction Monitoring * MSA MultiStage Activazion * MS/MS Tandem Mass Spectrometry * MSE Combination of MS and MS/MS in one single run (exact mass mode), [Plumb et al., 2006] * MSP MicroSphere Plate * MudPIT MUltiDimensional Protein Identification Technology (2D-LC) * NALDI Nano Assisted Laser Desorption Ionization * NetCDF NETwork Common Data Format * NICI Negative Ion Chemical Ionization * NMC Number of Missed Cleavages * NSAF Normalized Spectral Abundance Factor * NSD Nozzle-Skimmer Dissociation * NTM N-terminal Modification * NTT Number of Tryptic Termini / Number of enzymatically Tolerable Termini * oa-ToF orthogonal acceleration TOF * OBI-WARP Ordered Bijective Interpolated WARPing (chromatographic alignment) * Oi value correction factor used in APEX scoring * OLS Ontology Look-up Service * OMSSA Open Mass Spectrometry Search Algorithm * P3 Proteotypic Peptide Profiling * PAGE Polyacryl Amide gel Electrophoresis * PAI Protein Abundance Index * PAL Photo Affinity Labeling * PAR Protein Affinity Reagent * PATRIC Position And Time Resolved Ion Collector * PCER Per-Comparison Error Rate * PCP Protein Correlation Profiling * pcPIR Photo-Cleavable Protein Interaction Reporter * PCS Peptide-Concatenated Standard * PDA Photo Diode Array * PFER Per-Family Error Rate (PCER = FWER = PFER) * PFF Peptide Fragment Fingerprinting * PFP Peptide Fragmentation Pathway * PIC Photo-Induced Cross-Linking * PICI Positive Ion Chemical Ionization * PICR Protein Identifier Cross-reference Service * PIE Pulsed Ion Extraction * PIR Protein Interaction Reporter * PIT Percentage of Incorrect Target matches * PMF Peptide Mass Fingerprinting / Proton Mobility Factor * PMSS Peptide Match Score Summation * POI Protein Of Interest (in TDA approaches) * PQD Pulsed Q Collision-induced Dissociation * PrEST PRotein Epitope Signature Tag * PRM Parallel Reaction Monitoring * PSAQ Protein Standard Absolute Quantification * PSD Post Source Decay * PSI Proteomics Standards Initiative * PSICQUIC PSI Common Query InterfaCe * PSM Peptide Spectrum Match * PSMS Plasma Source Mass Spectrometry * PSP Proteomics Signature Profiling * PST Peptide Sequence Tag * PTH PhenylThioHydantoin (Edman-Abbau) * PTM Post Translational Modification * PTP ProteoTypic Peptide * PTR Proton Transfer Reaction * QconCat Quantification-conCATamere of tryptic Q-peptides * QET Quasi Equilibrium Theory * QITL Quantitation by Isobaric Terminal Labelling * QPrEST Quantification PRotein Epitope Signature Tag * ReACT Real-time Analysis for Cross-linked peptide Technology * reISD reflector mode In Source Decay * REMPI Resonance Enhanced Multiphoton Ionization * RFD RadioFlow Detection * RIA Relative Isotope Abundance * RIC Reconstructed Ion Chromatogram * RMM Relative Molecular Mass * RMS Reaction Mass Spectrometry * ROC Receiver Operating Characteristic * RP-HPLC Reverse Phase-High Performance Liquid Chromatography * RPKM Reads Per Kilobase of transcript per Million mapped reads * SAAV Single Amino Acid Variant * SAM Significance Analysis of Microarrays * SCX Strong Cation eXchange * SDS Sodium Dodecyl Sulfate * SEC Size Exclusion Chromatography * SELDI Surface Enhanced Laser Desorption and Ionization * SFC Supercritical Fluid Chromatography * SFMS Sector-Field Mass Spectrometer * SI Spectral Index * SIC Single Ion Current * SID Surface-Induced Dissociation * SID-SRM Stable Isotopic Dilution - SRM (Selected Reaction Monitoring) * SIDT Single Ion in Droplet Theory * SIFT Selected Ion Flow Tube * SIL Stable Isotopically Labelled * SILAC Stable Isotope Labeling with Amino acids in Cell culture * SILAM Stable Isotope Labeling of Mammals * SILAP Stable Isotope LAbeled Proteome * SIM Selected Ion Monitoring (only precursor) / Single Ion Monitoring * SIMS Secondary Ion Mass Spectrometry * SILAP Stable Isotope Labeled Proteome * SILE Stable Isotope Labelling Experiment * SIS Stable Isotope-labeled Standard peptide * SISCAPA Stable Isotope Standards and Capture by AntiPeptide antibodies * SLIM Simple Light Isotope Metabolic labelling * SLoMo Site Localization of Modifications * SNAP Sophisticated Numerical Annotation Procedure * SNR Signal-to-Noise Ratio * SNOC S-NitrosOCystein * SORI Sustained Off-Resonance Irradiation * SPC Shared Peak Count * SPE Solid Phase Extraction * SPS Shotgun Protein Sequencing * SPMDB Standard Protein Mix DataBase * SQID SeQuence IDentification (a peptide score) * SQMS Scanning Quadrupole Mass Spectrometry * SORI-CID Sustained Off-Resonance Irradiation Collision-Induced Dissociation * SRM Single / Selected Reaction Monitoring (precursor and product) * SS-MS Spark Source Mass Spectrometry * SSI Sonic Spray ionization * STED Stimulated Emission Depletion * STS Sequence Tagged Search * SWATH Sequential Windowed Aquisition of all THeoretical mass spectra/ions; a DIA (Data Independent Aquisition) method; means a series of isolation windows * SWIFT Stored Waveform Inverse Fourier Transform * TAILS Terminal Amine Isotopic Labeling of Substrates * TAP Tandem Affinity Purification * TDA Target Dependent Acquisition (SRM / MRM) * TEDE Thioester Dead End * Th 1 Thomson = 1U / 1e * TIC Total Ion Current / Chromatogram * TIMS Thermal Ionization Mass Spectrometry * TIQAM Targeted Identification for Quantitative Analysis by MRM * TIS Timed Ion Selector * TLC Thin Layer Chromatography * TLF Time Lag Focussing * TMT Tandem Mass Tag * TOF Time Of Flight * TOPP OpenMS Proteomic Pipeline * TPP Trans Proteomic Pipeline * TQMS Triple Quadrupole Mass Spectrometry * TWIG Travelling Wave Ion Guide * TWIMS Travelling Wave Ion Mobility Spectrometer * UHPLC Ultra High Pressure Liquid Chromatography * ULOQ Upper Limit Of Quantification * UPLC Ultra Performance Liquid Chromatography * VOC Volatile Organic Compound * WAX Weak Anion Exchange * XIC eXtracted Ion Chromatogram * XL-MS Cross-Linking Mass Spectrometry Look also at the following mass spectrometry acronym lists: ===========================================================
Wikipedia
Little encyclopedia of mass spectrometry, Uni HD
Wiley (Proteomics) collection of abbreviations
IUPAC MS terms
Standard definitions of terms relating to mass spectrometry
Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013)
IonSource MS Terms and Definitions
MS Adduct Ions list
