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  LC-MS Application Notes: Solutions Index Page
 To download or view application notes, please select one of the categories by name below or scroll down this page.
 


Proteomics 

App. note 412: A New Methodology for Targeted Peptide Quantitation in Complex Mixtures Using   App. note 412: A New Methodology for Targeted Peptide Quantitation in Complex Mixtures Using a High Resolution Triple Quadrupole Mass Spectrometer
 
 

Author(s): Reiko Kiyonami, Scott Peterman, Rosa Viner, Amol Prakash, and Vlad Zabrouskov, Thermo Fisher Scientific, San Jose, CA

 
 

  App. Note 386: Advantages of the LTQ Orbitrap for Protein Identification in Complex Digests
 
 

Author(s): Rosa Viner, Terry Zhang, Scott Peterman, and Vlad Zabrouskov, Thermo Fisher Scientific, San Jose, CA, USA

 
 

  App. Note 380: Targeted Quantitive Protein Analysis in Human Serum, Using High Resolution Multiple Selected Reaction Monitoring Assays
 
 
Author(s): Reiko Kiyonami, Scott Peterman, and Ken Miller, Thermo Fisher Scientific, San Jose, CA, USA 
 
 

  App. Note 363: Analysis of a Complex Sample of Bacterial Whole Cell Lysate from Haemophilus ducreyi Using the LXQ
 
 
Author(s): Kai Scheffler, Ph. D., Thermo Fisher Scientific GmbH, Dreieich, Germany
 
 

  App. Note 360: Increased Coverage in the Transmembrane Domain with Activated Ion ECD for Top-down FTMS of Integral Membrane Proteins
 
 
Author(s): Vlad Zabrouskov,1 Jennifer Zhang,1 Thomas D. McClure,1 Julian P.Whitelegge2, 1Thermo Fisher Scientific, San Jose, California, USA; 2The Pasarow Mass Spectrometry Laboratory, The Departments of Psychiatry and Biobehavioral Sciences, Chemistry and Biochemistry and The Jane & Terry Semel Institute for Neuroscience and Human Behavior, The Molecular Biology Institute and The Brain Research Institute, UCLA, Los Angeles, California, USA
 
 

  App. Note 357: Site-Specific Identification of 3-Nitrotyrosine and Nitrosocysteine Residues in Peptides Using MALDI Mass Spectrometry
 
 
Author(s): Victor Sharov and Christian Schöneich; University of Kansas School of Pharmacy, Lawrence, KS, USA; Zhiqi Hao, Rosa Viner, Roger Biringer and Andreas Hühmer; Thermo Fisher Scientific, San Jose, CA, USA
 
 

  App. Note 345: Proteomics in ADME Tox Studies: High-Throughput Identification and ESI Linear Ion Trap Mass Spectrometry with 2D-DIGE
 
 
Author(s): Ola Rönn1, Johan Öhman1, Daniel Haid1, Helena Nordvarg1, Lena Hörnsten1, John Flensburg1, Erik Forsberg1, David Fenyö1,Hélèn Bergling1, Gary Woffendin2, and Michaela Scigelova2 (1GE Healthcare, Uppsala, Sweden; 2Thermo Fisher Scientific, Hemel Hempstead, UK)
 
 

  App. Note 344: Top-Down Analysis of the Low Molecular Weight Human Plasma Proteome Using Hybrid Ion Trap-Fourier Transform Mass Spectrometry
 
 
Author(s):  Jennifer N. Sutton1,5 , Leo E. Bonilla1, Tori Richmond1, Robert E. Gerszten2, Emerson Liu2, Xui Shi2, Michael Senko3, Vladimir Zabrouskov3, Neil L. Kelleher4, Andrew Forbes4, Robert G. Harper5 (1Biomarker Research Initiatives in Mass Spectrometry (BRIMS) Center, Thermo Fisher Scientific, Boston, MA; 2Cardiology Division and Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA; 3Thermo Fisher Scientific, San Jose, CA; 4Center forTop Down Proteomics, Department of Chemistry, University of Illinois, Urbana, IL; 5Department of Chemistry,WestVirginia University, Morgantown,WV)
 
 

  App. Note 338: Identification of Glycosylated Peptides from Data Dependent Neutral Loss Scans Using a Linear Ion Trap Mass Spectrometer
 
 
Author(s): Gargi Choudhary, Jae Schwartz, and Diane Cho, Thermo Fisher Scientific, San Jose, CA Edited by: Wendy Schaeffer, Thermo Fisher Scientific, San Jose, CA
 
 

  App. Note 335: Characterization of Protein Glycosylation Using ESI ChipTM Static Nanospray Ion Trap MSn Mass Spectrometry 
 
 
Author(s): Dirk Chelius1 and Sheng Zhang2; (1Thermo Fisher Scientific, San Jose, CA; 2Advion BioSciences, Inc., Ithaca, NY)
 
 

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ADME/Tox

App. note 415 Experimental Strategies for Determining the Distribution of Erlotinib in Pancreatic Tumors by MALDI Using an LTQ Linear Ion Trap Mass Spectrometer   App. note 415 Experimental Strategies for Determining the Distribution of Erlotinib in Pancreatic Tumors by MALDI Using an LTQ Linear Ion Trap Mass Spectrometer
 
 

Author(s): M.C. Prieto Conaway1, H. Bui1, S. Beachy2, R. Pitoniak2, B. Hylander2, P.Wang2, K. Marlar2, E. Repasky2, L. Kazim2, 1Thermo Fisher Scientific, San Jose, CA, USA; 2Roswell Park Cancer Institute, Buffalo, NY, USA

 
 

  App. Note 406: Study of Free Radical Fragment Ions Generated from ESI-CID-MS/MS Using LTQ and LTQ Orbitrap Mass Spectrometers
 
 
Author(s):  Guifen Xu1, Tom Huang1, Jennifer Zhang2, Thomas D. McClure2, and Shichang Miao1 * 1 PKDM Department, Amgen SSF, South San Francisco, CA USA; *Analytical Chemistry and DMPK, ChemoCentryx Inc., Mountain View, CA USA; 2Thermo Fisher Scientific, San Jose, CA USA
 
 

App. note 413: The Distribution of Metabolites of Di-(2-ethylhexyl) Phthalate on a Whole Rat by Imaging MS Using a MALDI Ion Trap   App. note 413: The Distribution of Metabolites of Di-(2-ethylhexyl) Phthalate on a Whole Rat by Imaging MS Using a MALDI Ion Trap
 
 

Author(s): T.A. Snow,1 M.Prieto Conaway,2 H. Bui,2 W.J.Fasano,1 L.A. Manning1, 1DuPont Haskell Laboratory, Newark, DE, USA; 2Thermo Fisher Scientific, San Jose, CA, USA

 
 

  App. Note 358: Highly Selective Detection and Identification of Nitrofurans Metabolites in Honey Using LC-MS/MS
 
 
Author(s): Eduardo Matus,1 Jean-Jacques Dunyach,2 Alejandro Albornoz3; 1Food Science Laboratories, Buenos Aires, Argentina; 2Thermo Fisher Scientific, San Jose, CA; 3Eidomet, Buenos Aires, Argentina
 

  App. Note 346: MS MS as an LC Detector for the Screening of Drugs and Their Metabolites in Race Horse Urine 
 
 
Author(s): Gargi Choudhary and Diane Cho, Thermo Fisher Scientific; Wayne Skinner and Scott Stanley, University of California–Davis
 

 
  App. Note 345: Proteomics in ADME Tox Studies: High-Throughput Identification and ESI Linear Ion Trap Mass Spectrometry with 2D-DIGE
 
 
Author(s): Ola Rönn1, Johan Öhman1, Daniel Haid1, Helena Nordvarg1, Lena Hörnsten1, John Flensburg1, Erik Forsberg1, David Fenyö1,Hélèn Bergling1, Gary Woffendin2, and Michaela Scigelova2 (1GE Healthcare, Uppsala, Sweden; 2Thermo Fisher Scientific, Hemel Hempstead, UK)
 

 

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Biomarkers
  App. Note 380: Targeted Quantitive Protein Analysis in Human Serum, Using High Resolution Multiple Selected Reaction Monitoring Assays
 
 
Author(s): Reiko Kiyonami, Scott Peterman, and Ken Miller, Thermo Fisher Scientific, San Jose, CA, USA 
 

 
  App. Note 343: Identification and Differential Expression Analysis of Putative and Known Plasma Biomarkers for Human Hypertrophic Cardiomyopathy
 
 

Author(s): Tori Richmond1, Manor Askenazi1, Leo Bonilla1, Robert E. Gerszten2, Jennifer Sutton1, Emerson Liu2, David Sarracino3 (1Biomarker Research Initiatives in Mass Spectrometry (BRIMS) Center, Thermo Fisher Scientific, Boston, MA; 2Cardiology Division and Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA; 3Harvard-Partners Center for Genetics and Genomics, Cambridge, MA)

 

 

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Environmental and Food Safety
  App. Note 407: Simple and Rapid Analysis of Chloramphenicol in Milk by LC-MS/MS
 
 
Author(s):  Ting Liu1, Peter Wang1, and Kefei Wang2 , 1 Thermo Fisher Scientific, Shanghai, China; 2Thermo Fisher Scientific, San Jose, CA, USA
 
 

  App. Note 403: Analysis of Chloroacetanilide and Other Acetamide Herbicide Degradates In Drinking Water (EPA Method 535) by LC-MS/MS
 
 
Author(s): Jonathan Beck , Thermo Fisher Scientific, San Jose CA
 
 

App. Note 395: The Use of FAIMS to Separate Loperamide from PEG Prior to MS Analysis Using an LTQ XL   App. Note 397: Determination of Sulfonamide Antibiotics in Wastewater by Liquid Chromatography
 
 
Author(s):  Eleni Botitsi, Charalampia Frosyni, and Despina Tsipi; General Chemical State Laboratory, Athens, Greece
 
 

App. Note 391: Analysis of Regulated Pesticides in Drinking Water   App. Note 391: Analysis of Regulated Pesticides in Drinking Water Using Large Volume Injections, Online Pre-concentration, and Fast-HPLC with EQuan
 
 
Author(s): Jonathan R. Beck and Charles Yang ; Thermo Fisher Scientific, San Jose, CA
 
 

  App. Note 387: Multi-residue Analysis of Pesticides in Food Using GC/MS/MS with the TSQ Quantum GC
 
 

Author(s): Kuniyo Sugitate, Michiko Kanai, Thermo Fisher Scientific, Yokohama, Japan, Masahiro Okihashi, Division of Food Chemistry, Osaka Prefectural Institute of Public Health, Osaka, Japan, Dipankar Ghosh, Thermo Fisher Scientific, San Jose, CA, USA

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  App. Note 379: Analysis of Microcystins from Blue-green Algae Using the TSQ Quantum Ultra LC-MS/MS System
 
 
Author(s): Jonathan Beck, Thermo Fisher Scientific, San Jose, California, USA,  Mihoko Yamaguchi and Kaori Saito, Thermo Electron K.K., Yokohama, Japan 
 
 

  App. Note 378: Quantitation Enhanced Data-Dependent (QED) Scanning of Drinking Water Samples Using EQuan for Pesticide Analysis on a Triple Stage Quadrupole
 
 
Author(s): Mihoko Yamaguchi, Thermo Fisher Scientific, Yokohama, Japan   
 
 

  App. Note 372: LC/MS/MS Analysis of Anti-Infectives In Raw and Treated Sewage
 
 
Author(s): P.A. Segura1, A. Garcia Ac1, A. Lajeunesse2, D. Ghosh3, C. Gagnon2 and S. Sauvé1, 1 Département de Chimie, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada H3C 3J7, 2 Centre Saint-Laurent, Environnement Canada, 105, rue McGill, Montréal, QC, Canada H2Y 2E7, 3 Thermo Fisher Scientific, San Jose, CA, USA
 
 

  App. Note 361: Determination of Trace Level Nitrofuran Metabolites in Crawfish Meat by Electrospray LC-MS/MS on the TSQ Quantum Discovery MAX
 
 
Author(s): Tao Ding,1 Jingzhong Xu,1 Chongyu Shen1 and Kefei Wang2 1 Food Laboratory, APFIC, Jiangsu Entry-Exit Inspection and Quarantine Bureau of People’s Republic of China, Nanjing, China 2 Thermo Fisher Scientific, San Jose, CA, USA
 
 

  App. Note 358: Highly Selective Detection and Identification of Nitrofurans Metabolites in Honey Using LC-MS/MS
 
 
Author(s): Eduardo Matus,1 Jean-Jacques Dunyach,2 Alejandro Albornoz3; 1Food Science Laboratories, Buenos Aires, Argentina; 2Thermo Fisher Scientific, San Jose, CA; 3Eidomet, Buenos Aires, Argentina
 
 

  App. Note 355: Utility of H-SRM to Reduce Matrix Interference in Food Residue Analysis of Pesticides by LC/MS/MS Using the TSQ Quantum Discovery
 
 
Author(s):  Yoko Yamagishi, Thermo Fisher Scientific, Yokohama, Japan  
 
 

  App. Note 319: Quantitation of Acrylamide in Food Samples on the TSQ Quantum Discovery by LC/APCI-MS/MS
 
 
Author(s): Kevin J. McHale, Witold Winnik and Gary Paul, Thermo Fisher Scientific, Somerset, NJ, USA
 
 

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Bioanalysis
  App. Note 401: Comparing Manual Compound Optimizations Against Automated Optimizations Obtained by QuickQuan on the TSQ Quantum Access
 
 
Author(s): Nicholas Duczak and Jim Koers, Thermo Fisher Scientific, San Jose CA
 
 

  App. Note 400: Chemical Background Removal in the Determination of Linoleic Acid Using LC-FAIMS-MS
 
 
Author(s): Uddhav Kelavkar and Justin Hutzley, University of Pittsburgh, Pittsburgh, PA; Jonathan McNally, Thermo Fisher Scientific, San Jose, CA; James Kapron, Thermo Fisher Scientific, Ottawa, CN
 
 

  App. Note 399: The Impact of the Reversed Energy Ramp Scan Function on Metabolite Identification at or Below the 1 µM Level
 
 
Author(s): Louis Maljers, Thermo Fisher Scientific, San Jose, CA, USA
 
 

App. Note 394: Improved Signal-to-Noise Ratio in the Antidoping Analysis of Clenbuterol   App. Note 394: Improved Signal-to-Noise Ratio in the Antidoping Analysis of Clenbuterol in Urine Using LC –FAIMS–H-SRM
 
 
Author(s):  James Kapron1 and Rohan Thakur2; 1Thermo Fisher Scientific, Ottawa, Canada; 2Thermo Fisher Scientific, San Jose, CA, USA
 
 
 


  App. Note 388: Determination of Estradiol in Plasma with Negative Chemical Ionization GC-MS/MS on TSQ Quantum GC
 
 

Author(s): Hans Schweingruber, BC Cha, Ethan Chan, Kefei Wang, Thermo Fisher Scientific, San Jose, CA, USA 

 
 

App. Note 382: Stable Isotope Labeled FattyAcid Analysis in Plasma   App. Note 382: Stable Isotope Labeled Fatty Acid Analysis in Plasma Using LC-FAIMS-SRM
 
 
Author(s): Kevin Bateman1, Sebastien Gagne1, Sheldon Crane1, Jean-Francois Levesque1, and James T. Kapron2; 1Merck Frosst Centre for Therapeutic Research, Kirkland, Quebec, Canada; 2Thermo Fisher Scientific, Ottawa, Canada
 
 

  App. Note 376: Mechanism of [M+H]+ Formation in Atmospheric Pressure Photoionization Mass Spectrometry
 
 
Author(s): Amin Kamel and Kevin Colizza, Department of Exploratory Medicinal Sciences, Pfizer PGRD, Groton, CT;  Patrick Jeanville, Thermo Fisher Scientific, Miami, FL
 
 

  App. Note 375: Collisionally-Induced Dissociation of Methimazole and Acetylsalicylic Acid: Proposed Mechanisms of Ion Formation Using Hydrogen/Deuterium Exchange
 
 
Author(s): Amin Kamel and Kevin Colizza, Department of Exploratory Medicinal Sciences, Pfizer PGRD, Groton, CT; Patrick Jeanville, Thermo Fisher Scientific, Miami, FL  
 
 

  App. Note 374: Mechanisms of Ion Formation for Famotidine and Azithromycin Using Hydrogen/Deuterium Exchange and High Resolution Mass Measurements
 
 
Author(s): Amin Kamel and Kevin Colizza, Department of Exploratory Medicinal Sciences, Pfizer PGRD, Groton, CT; Patrick Jeanville, Thermo Fisher Scientific, Miami, FL 
 
 

  App. Note 362: Selectivity Improvement for Drug Urinalysis Using FAIMS and H-SRM on the TSQ Quantum Ultra
 
 
Author(s): James Kapron and David A. Barnett; Thermo Fisher Scientific, Ottawa, ON, Canada
 
 

  App. Note 350: Rapid Quantitative and Confirmational Screening for Drugs in Race Horse Urine by ESI-LC/MS/MS and MS/MS/MS
 
 
Author(s): Patrick Russell,1 Paul Steinberg,2 Mary L. Blackburn,2 Diane Cho,2 Robert Heather2 (1University of Florida, Racing Laboratory, Gainesville, Florida; 2Thermo Fisher Scientific, San Jose, California)
 
 

  App. Note 349: Measurement of Metabolic Stability Using SIM and Identification of Metabolites by Data Dependent Full-Scan MS/MS and CNL Scanning
 
 
Author(s): Peter B Ehmer, Ethirajulu Kantharaj, Katie De Wagter, Anne Van Vlaslaer, Claire Mackie and Ron AHJ Gilissen; Department of ADME/Tox, In Vitro Pharmacokinetics Group, Johnson & Johnson Pharmaceutical Research & Development, 2340 Beerse, Belgium; Dipankar Ghosh and Karel Lazou; Thermo Fisher Scientific, San Jose, CA, USA
 
 

  App. Note 348: Identification of Phase I Biotransformation Products of Buspirone Using Parent Ion Scanning Triggered Data Dependent MS/MS
 
 
Author(s): Kevin J. McHale, Scott M. Peterman and Mark R. Kagan; Thermo Fisher Scientific
 
 

  App. Note 347: Applying Highly-Selective Reaction Monitoring (H-SRM) for the Assay of Midazolam and 1-Hydroxymidazolam in Plasma on the TSQ Quantum Ultra
 
 
Author(s): Kevin J. McHale and Nick Duczak, Jr.; Thermo Fisher Scientific, Somerset, NJ, USA  
 
 

  App. Note 337: Trace-Level Quantitation of Chloramphenicol Using the TSQ Quantum Discovery
 
 
Author(s): Kevin J. McHale, Thermo Fisher Scientific, Somerset, NJ, USA
 
 

  App. Note 336: Ultra-sensitive LC/MS/MS Quantitation of Lipids in Biological Fluids
 
 
Author(s): Seon Hwa Lee,1 Kevin J. McHale,2 Michelle Williams,1 and Ian A. Blair1 (1University of Pennsylvania, Philadelphia, PA; 2Thermo Fisher Scientific, Somerset, NJ)
 
 

  App. Note 314: Fast Quantitative Analysis of Pergolide Using APCI on the TSQ Quantum Discovery
 
 

Author(s): Nicola Hughes,1 Antony Harvey,2 Witold Winnik,3 and Gary Paul3 (1Biovail Contract Research, Toronto, Ontario, Canada; 2Thermo Fisher Scientific, San Jose, CA, USA; 3Thermo Fisher Scientific, Somerset, NJ, USA)

 
 

  App. Note 310: Improved Quantitative Selectivity of Clenbuterol in Human Urine Using High Resolution on the TSQ Quantum Mass Spectrometer
 
 

Author(s): Mark Churchill1, Mark Harrison1, John Henninge,2 and Hanne Lund2 (1Thermo Fisher Scientific, Stafford House, 1 Boundary Park, Boundary Way, Hemel Hempstead, HP2 7GE, UK; 2Aker University Hospital, Hormone Laboratory, Section for Doping Analysis, Trondheimsveien, N-0514, Oslo, Norway)

 
 

  App. Note 309: Quantitation of Cabergoline at Extremely Low Plasma Concentrations with a Triple Quadrupole Mass Spectrometer
 
 

Author(s): Nicola Hughes,1 Antony Harvey,2 Witold Winnik,3 Jean-Jacque Dunyach,2 Ma’an Amad,2 Maurizio Splendore,2 and Gary Paul3(1Biovail Contract Research, Toronto, Ontario, Canada;2Thermo Fisher Scientific, San Jose, CA, USA; 3Thermo Fisher Scientific, Somerset, NJ, USA Systemic Plasma Analysis)

 
 

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Clinical and Toxicology

 

App. note 416: A Quantitative, Efficient Method for Analysis of 25-Hydroxy-Vitamin D3 and 25-Hydroxy- Vitamin D2 Using TurboFlow Technology   App. note 416: A Quantitative, Efficient Method for Analysis of 25-Hydroxy-Vitamin D3 and 25-Hydroxy- Vitamin D2 Using TurboFlow Technology
 
 

Author(s): Allen Zhang, Robert Kane, Francois Espourteille, Thermo Fisher Scientific, Franklin, MA

 
 

  App. Note 409: A Complete General Unknown Screening Workflow for Analysis of Drugs and Toxic Compounds in Urine Using LC-MS
 
 
Author(s): Taha Rezai1, Marta Kozak1, Kate Torchlin2; 1 Thermo Fisher Scientific, San Jose, CA; 2Thermo Fisher Scientific, Franklin, MA 
 
 

App. Note 395: The Use of FAIMS to Separate Loperamide from PEG Prior to MS Analysis Using an LTQ XL   App. Note 396: Quantitative Analysis of 25-OH-D2 and 25-OH-D3 in Serum by LC-MS/MS
 
 
Author(s): Marta Kozak, Thermo Fisher Scientific, San Jose, CA
 
 

  App. Note 390: A Quantitative Screen for Multiple Classes of Illicit Drugs and Their Primary Metabolites in Human Biological Fluids by LC-MS/MS
 
 
Author(s): Kevin J. McHale,1 Joyce Ho,2 and Angela Springfield2; 1Thermo Fisher Scientific, Somerset, NJ, USA; 2Tarrant County Medical Examiner, Fort Worth, TX, USA 
 
 

  App. Note 384: Determination of Digoxin in Serum by Liquid Chromatography–Tandem Mass Spectrometry
 
 

Author(s): François-Ludovic Sauvage1, Pierre Marquet1,2; 1Department of Pharmacology-Toxicology, University Hospital, Limoges, France; 2Laboratory of Pharmacology, Faculty of Medicine, University of Limoges, France. 

 
 

  App. Note 383: Determination of LSD and Its Metabolites in Human Biological Samples by Liquid Chromatography–Tandem Mass Spectrometry
 
 
Author(s): François-Ludovic Sauvage1, Pierre Marquet1,2; 1Department of Pharmacology-Toxicology, University Hospital, Limoges, France; 2Laboratory of Pharmacology, Faculty of Medicine, University of Limoges, France. 
 
 

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