MS_Abbreviations.txt

List of MS-related abbreviations:
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* 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 für 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:
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 [http://en.wikipedia.org/wiki/List_of_mass_spectrometry_acronyms Wikipedia]
 [http://www.rzuser.uni-heidelberg.de/~bl5/encyclopedia.html Little encyclopedia of mass spectrometry, Uni HD]
 [http://onlinelibrary.wiley.com/doi/10.1002/pmic.201370055/pdf Wiley (Proteomics) collection of abbreviations]
 [http://mass-spec.lsu.edu/msterms/index.php IUPAC MS terms]
 [http://www.iupac.org/nc/home/projects/project-db/project-details.html?tx_wfqbe_pi1%5bproject_nr%5d=2003-056-2-500 Standard definitions of terms relating to mass spectrometry]
 [http://www.mssj.jp/8507x1515.pdf Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013)]
 [http://www.ionsource.com/links/definitions.htm IonSource MS Terms and Definitions]
 [http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator MS Adduct Ions list]