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Time of Flight Mass Spectrometry for The Modern Lab: Qualitative Analysis, Quantitative Measurement and Rapid Screening and Identification

This article explains the use of a TOF‑MS system that provides an MS technology that enables the scientist to rapidly screen, identify and quantify compounds with accurate mass, screening speed and ease of use.


MS Solutions #1: Quantitation in hyphenated chromatographic techniques

Mass spectrometry has long been a valuable quantitative tool used across many industries for numerous applications including food, beverage, pharma and environmental analysis. Its utility ranges from use as an alternative detector to UV in LC for difficult non-chromophoric analytes to those applications that fully exploit the extra resolving power or sensitivity that mass spectrometry can afford.


MS Solutions #9: Peptide Sequencing with Electrospray LC/MS Part 1: Ion Types and Nomenclature

One of the most significant and important applications for mass spectrometry is the sequencing of polypeptides by electrospray LC/MS. An error in the sequence or the substitution of one amino acid with another can completely alter the biological function of a peptide molecule. Determination of sequences is therefore a vital part of biomedical research, proteomics, and the manufacture of peptide-based drug substances. We will discuss the basics of peptide sequencing with mass spectrometry in the next three issues of MS Solutions.


MS Solutions #10: Peptide Sequencing with Electrospray LC/MS Part 2: Interpretation of a Simple Spectrum

In the last issue of MS Solutions we discussed MS/MS fragmentation of polypeptides, the types of ions formed, and the mechanism of their formation. In this article we will examine a tandem mass spectrum of a simple polypeptide and step through an interpretation strategy leading to the complete sequence determination.


MS Solutions #16: Determination of Intact Protein Molecular Mass from Multiple-Charge Electrospray Mass Spectra

In two previous instalments of MS Solutions, I discussed the sequencing of simple, single-charge peptide ions using MS/MS. In this and another upcoming edition I am going to discuss the use of multiple-charge ions in protein and peptide analysis.


MS Solutions #19: AMDIS – An Introduction to Extracting High-Quality Spectra from Complex GC/MS Data

The identification of components by GC/MS in complex mixtures has essentially two parts – extracting a spectrum that is due to a single component and then identifying the component, usually through a library search of the unknown spectrum. Identification is typically the result of searching large libraries and high-quality search algorithms and has been discussed in a previous series [NIST 11- O. David Sparkman]. Unfortunately, if the spectrum sent to the library search routine is not from a single component or is missing major mass spectral peaks, the answer from the library search has far less confidence. For many applications it is sufficient to simply allow the instrument data system – sometime with operator assistance – to average over a peak and take a nearby region as a background for subtraction. For chromatographically isolated components, this is a reasonable, although laborious approach; however, with complex chromatograms the problem can become impossibly to reasonable effect such manual deconvolutions. The spectrum that is extracted may have mass spectral peaks from adjacent components or the background subtraction may remove or diminish peaks that are a part of the spectrum.


MS Solutions #18: Use of ECD and ETD Fragmentation Mechanisms for Peptide Sequencing

In the previous instalment of MS Solutions, I described some of the problems encountered with collisionally-activated dissociation (CAD) of peptides when used in MS/MS sequencing experiments. We noted that the number and type of structurally significant ions produced is dependent on the sequence of amino acid residues. Some sequences, most notably those containing a a C-terminal arginine, result in very little in the way of useful MS/MS spectra.


MS Solutions #21: AMDIS — Setting Up and Running a Deconvolution and Target Analysis: Part 3

In the first two parts of the discussion of setting up AMDIS the basics of running an analysis with retention index filtering as well as a simple analysis were discussed. In this final part of the set up section, instrument settings and filtering will be covered.  


How to Analyse Unknown Samples by Pyrolysis GC/MS?

Although GC/MS and LC/MS are very powerful analytical techniques, they generally lack the ability to analyse and characterize insoluble materials, such as polymers and other high molecular weight products. An elegant approach to cope with this type of samples involves a combination of thermal decomposition and online chromatographic analysis of the released breakdown products. This approach is called analytical pyrolysis.


How to Develop a Method using In-tube Extraction (ITEX) For GC and GC/MS?

Throughout our lives we are continuously exposed to substantial quantities of volatile organic components (VOC). Residual solvents from carpets, paints and glues largely determine the quality of the indoor air we daily inhale. Offices, workspaces and even our living rooms, it’s practically impossible to breathe clean air nowadays. Perhaps we are luckier with the food we eat and the beverages we drink? Unfortunately, I am afraid not. Solvents from packaging foils and printing inks may pose a severe risk for the foodstuff they contain, while the water we drink or use to make soda, beers, etc. is polluted with traces of disinfection agents and other environmental contaminants. No wonder ‘VOC analysis’ plays such a vital role in many QC laboratories around the globe.


Optimisation of Existing Methods for Analysis of Antibiotics in Meat using MS/MS Detection

The accurate detection and analysis of residual antibiotics in meat for human consumption is of critical importance in ensuring strict adherence to regulatory requirements for food safety. This article – the first in a series of features considering the detection of contaminants in meat – describes the optimization of an existing detection methodology that results in increased throughput by 5–10-fold, and more accurate and reproducible results, ensuring the best possible quantitation.


High Volume Mass Spectrometry Proteomics Results Require Robust Platforms and Powerful Software

Q: Making sense of the vast amount of data generated in mass spectrometry-based proteomics now requires computing power far beyond what ordinary desktop PCs can offer. Are there specialized IT infrastructure solutions available to still efficiently and accessibly manage this data?


Highly Sensitive Mass Spectrometry without Compromising Speed or Selectivity

Q: “In order to screen for both known and unknown compounds in a sample, high sensitivity is required. However, this is often to the detriment of selectivity and speed. Is there a technology available that optimizes sensitivity while maintaining necessary levels of speed of analyses and selectivity?”


Characterization of Chinese Medicines by Comprehensive Two-Dimensional Gas Chromatography and Time-of-Flight Mass Spectrometry (GC×GC-TOFMS) with Assistance of Multivariate Data Analyses

A comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS) system was applied for profiling the complex chemical composition of Chinese herbs (Radix Angelicae Pubescentis and Radix Angelicae Dahuricae ). The two-dimensional GC and deconvolution algorithm largely enhances selectivity and sensitivity of analysis. Over 300 compounds were identified in each herbal. The data obtained were then processed by multivariate data analyses. Based on their fingerprint chromatograms, herbs could be distinguished; e.g., by their species, geographical origins. GC×GC-TOFMS has shown great potential as a powerful tool for metabolomics studies.


Detection of Pharmaceuticals, Personal Care Products, and Pesticides in Water Resources by APCI-LC-MS/MS

In the method presented here, solid phase extraction (SPE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are utilized for the simultaneous determination of trace levels of compounds from a diverse group of organic wastewater contaminants.


Multi-residue Pesticide Analysis in Rice by QuEChERS and GC/MS Analysis

This article discusses current legislation governing the concentration of pesticide residues in foods and describes the QuEChERS sample preparation method. An application example is used to highlight the efficiency of the QuEChERS/ion trap GC/MSn technique, covering preparation of extracts and optimization of analytical parameters for injection, separation and detection.


High-throughput Screening Method for Multiple Classes of Antibiotics in Milk

Veterinary drugs are widely used to prevent the outbreak of disease in livestock and are commonly found in feed additives or in drinking water. In addition, veterinary drugs are given to treat diseases, for drying-off purposes or to prevent losses during transportation.


Combining Time of Flight Mass Spectrometry with Gas Chromatography for Increased Sensitivity in Beer Analysis

Beer is derived from natural plant products, mainly cereal grains such as barley, rice, wheat and corn. Beer samples are very complex and contain many hundreds of organic components including vitamins, amino acids, proteins and bitter acids. The ‘signature’ flavour and aroma of each particular beer brand is characterized by a vast array of volatile compounds, which often have very low olfactory thresholds. This means that the actual concentrations of signature compounds can be extremely low, posing significant analytical challenges. In addition, some compounds may exist at very high concentrations. As a result, beer samples can be very difficult to analyse.


Method 8260C by Purge and Trap Gas Chromatography–Mass Spectrometry

The improvement and protection of the environment from human activity is recognized by many as a duty we owe to future generations. Organizations such as the US Environmental Protection Agency (EPA) are created to provide guidance for the protection of the natural environment through regulation of pollution and analytical methodology.


MS Solutions #6: The Role of Isotope Peak Intensities Obtained Using Mass Spectrometry in Determining an Elemental Composition, Part 2

An illustrative example of the use of isotope peak ratios to determine an elemental composition taken with permission from Chapter 5 of "Introduction to Mass Spectrometry: Instrumentation, Applications and Strategies for Data Interpretation", 4th Ed., Wiley: Chichester, UK, 2007 by J. Throck Watson and O. David Sparkman.


MS Solutions #17: The Importance of Multiple-Charge Ion Precursors in Peptide MS/MS Sequencing

We typically think of a mass spectrum as consisting of a precursor ion at high m/z and a series of increasingly lower m/z product (fragment) ions. These types of mass spectra are shown in training courses and textbooks as didactic examples because they are easy to interpret “by hand”. A spectrum with these characteristics arises from the selection of a single-charge precursor ion. However, these teaching examples can be misleading to the beginning mass spectrometrist who may come to believe that any proper MS/MS experiment begins with selection of a single-charge precursor. In this article we will show that use of multiple-charge precursor ions is useful (and often essential), to obtain best results, particularly for peptide sequencing experiments.


MS Solutions #4: Dealing with Metal Adduct Ions in Electrospray: Part 2

Previously we discussed the fundamental issue of metal adduct ion formation in electrospray LC/MS including method development strategies for dealing with adduct ions. This month we will examine a real-world application which employs these strategies. A few years ago our laboratory developed a method for penicillin G by electrospray LC/MS.


Lipidomics Discovery Profiling and Targeted LC/MS Analysis in 3T3-L1 Differentiating Adipocytes

Lipidomics is a branch of metabolomics, the systems-based study of all lipids. Research in lipidomics typically involves identifying the way these molecules interact with other lipids, proteins and other metabolites, and their structure and function within the cell. The field of research to date has lagged behind that of genomics and proteomics, largely as a consequence of the complexity of lipids and the lack of powerful tools for their analysis. Recent advances in technology, particularly in the form of more advanced liquid chromatography and mass spectrometry systems, have enabled more detailed systems level analysis of lipids and their interacting partners [1]. These improvements have shed new light on a number of pathologies that result from lipid abnormalities, such as obesity and diabetes.


HPLC-MS-MS for Simultaneous Determination of Risperidone and 9-hydroxyrisperidone in Human Plasma: Application in a Bioequivalence Study

A highly sensitive, selective, accurate and precise method for simultaneous quantification of risperidone and 9-hydroxyrisperidone in human plasma was developed. The method was based on electrospray ion trap tandem mass spectrometry in multiple reaction monitoring mode. Risperidone, 9-hydroxyrisperidone and carbamazepine, an internal standard, were extracted from plasma by a single step extraction with ether after the addition of sodium hydroxide and sodium chloride. A 5-µL aliquot of the sample reconstituted in mobile phase was analysed on a C18 column at 30 ˚C with the mobile phase consisting of acetonitrile and ammonium acetate buffer pH 5.5 (35:65 v/v). The accuracy ranged from 99.29–104.5% and 95.05–101.0% of the true value for risperidone and 9-hydroxyrisperidone, respectively. The within-run and between-run precisions were less than 8.50%. The limit of quantitation was 0.1 ng/mL for both compounds. The calibration curves of risperidone and 9-hydroxyrisperidone were analysed by weighted least square linear regression with 1/x2 as a weighting factor. They were linear over the concentration range of 0.1–30 ng/mL with r2 of greater than 0.99. This developed method was successfully applied to a bioequivalence study of 2-mg risperidone tablets.


MS Solutions #15: NIST 11: What’s New and What Value Does it Offer? Part 5

This is the last in the five-part series about the features of NIST 11. This installment shows how spectra obtained by MS/MS methods from various soft ionization techniques, including those used with LC/MS can be searched against the NIST/EPA/NIH EI Mass Spectral Database and the results used to facilitate a structure determination.


MS Solutions #3: Dealing with Metal Adduct Ions in Electrospray: Part 1

The term “adduct ion” is a popular term among liquid chromatography/mass spectrometry (LC/MS) users to describe ions formed by adduction of alkali metal ions to an analyte molecule in positive ion analysis. However, the well-informed user should be aware that “adduct ion” correctly refers to any ion formed by adduction of an ionic species to a molecule. Therefore, the common protonated molecule or [M+H]+ is also properly called an adduct ion. In our column this month we will be discussing specifically the adduction of alkali metal ions (Na, K), to analyte molecules and will therefore use the term “metal adduct ion” to refer to these species.


UHPLC-MS: An Efficient Method for the Determination of Illicit Drugs

The illicit drugs trade generates one of the largest global revenues at around $322 billion, according to the UN World Drug Report, 2009 [1]. Posing a major threat to the pharmaceutical industry and patients worldwide, illicit drugs are falsified medicinal products that contain either sub-standard or falsified ingredients, or ingredients in the wrong dosage. The main illicit drugs are the opiates (mostly heroin), cocaine, cannabis, and amphetamine-type stimulants (ATS) such as amphetamines, methamphetamine and ecstasy. Illicit drugs are listed under five categories namely narcotics, stimulants, depressants, hallucinogens and cannabis. These categories include many drugs legally produced and prescribed by doctors as well as those illegally produced and sold outside of medical channels [2].


MS Solutions #11: NIST 11: What’s New and What Value Does it Offer? Part 1

The NIST 11 Mass Spectral Database, the successor to the NIST 08, is a fully evaluated collection of electron ionization (EI) Mass Spectra, which also includes a growing number of MS/MS Spectra and GC data. In this multi-part article, David Sparkman looks at history and current status of NIST 11 and explains its value to analytical scientists.


MS Solutions #12: NIST 11: What’s New and What Value Does it Offer? Part 2

The NIST 11 Mass Spectral database, the successor to the NIST 08, is a fully evaluated collection of electron ionization (EI) Mass Spectra, which also includes a growing number of MS/MS Spectra and GC data. In this multi-part article, David Sparkman looks at history and current status of NIST 11 and explains its value to analytical scientists.


MS Solutions #14: NIST 11: What’s New and What Value Does it Offer? Part 4

This installment in the series on NIST 11 is about the Incremental Name Search , replicate spectra, and the NIST GC Methods, and Retention Index Database.


MS Solutions #2: Improving Electrospray LODs by Decreasing Column Diameter

Reducing the internal diameter of your HPLC columns is an advantage for electrospray (ESI) LC/MS users. To understand this, two characteristics of ESI must be understood: (1) how response (i.e., peak area or height), is related to analyte concentration and (2) how response varies with HPLC flow rate.


MS Solutions #7: Adjusting Electrospray Voltage for Optimum Results

An electrospray LC/MS interface consists of an enclosed, atmospheric pressure chamber. The HPLC effluent enters this chamber through a capillary tube which is surrounded by a second, concentric tube through which a nebulizing gas is applied. In this article I will refer to this assembly as the LC capillary. Opposite from or, in modern designs, orthogonal to the incoming HPLC effluent is the inlet to the mass spectrometer. This inlet is usually a capillary tube as well and will be referred to hereafter as the MS inlet.


MS Solutions #20: AMDIS: Setting Up and Running a Deconvolution and Target Analysis – Part 1

AMDIS is designed to do analysis for target compounds in a GC/MS data file. To do the analysis you need a completed data file (AMDIS reads most current and many older instrument formats as well as standard formats such as netCDF and mzXML) and a target library. You can put a target library together from standards using AMDIS or by extracting spectra from another library such as NIST11. The download package (see end of article) contains a small library that can be used for the data files in the tutorial with the download package. The details of creating a library of your own will be covered in a later article. The examples used here will come from the tutorial package so that if you choose you may download the entire package and run the data for yourself (see end of article for download address).


MS Solutions #22: AMDIS – Setting Up and Running a Deconvolution and Target Analysis – Part 2

In the last part of this AMDIS discussion, the setting up and running of a simple analysis was discussed. However, to take full advantage of AMDIS it is far better to make use not only of the mass spectral information, but also the retention time data. In Part 2 of the “Setting Up and Running a Deconvolution and Target Analysis”, we will discuss setting up and using the retention information and briefly discuss the various parameters that can be set by the user.


MS Solutions #5: The Role of Isotope Peak Intensities Obtained Using Mass Spectrometry in Determining an Elemental Composition, Part 1

The atomic mass of an element is the weighted average of the masses of the naturally occurring isotopes of that element. These different isotopes of an element have
different masses that are almost an integer in value because of different numbers of
neutrons in their nuclei; e.g., carbon has two primary naturally occurring isotopes, 12C and 13C. These two isotopes have respective integer masses of 12 and 13. Atoms of 12C have one less neutron in their nuclei than do atoms of 13C. This means that a mass spectrum of an ion containing carbon will be represented by peaks that are one m/z unit apart. The lowest m/z value peak represents an ion where all the carbon atoms are 12C. The peak one integer m/z value higher represents an ion where one of the carbon atoms is 13C. The peak one m/z unit higher than that represents the ion where two of the carbon atoms are 13C and so on.


Simultaneous Measurement of Reduced and Oxidized Coenzymes Q9 and Q10 in Rat Tissues by LC-MS

A method for the determination of reduced and oxidized coenzymes Q9 and Q10 in rat tissues using LC-MS was developed. The chromatographic separation was performed on a reversed-phase column (4.6 × 250 mm, 4 μm) in an isocratic mode using a 2-propanol/acetonitrile (60/40 % v/v) mixture. 


Identification of Pesticide Residues in Orange Essential Oils by GC/MS

Determining the presence of pesticide residues in essential oils is very important for ensuring their quality, especially because many essential oils are used in food, pharmaceutical and cosmetic industries.


MS Solutions #23: AMDIS – Developing Libraries

For AMDIS to be as effective as possible, it is essential to have high quality target libraries. These can either come from standards taken with the same instrument that the data is analysed on or from the NIST library. In this article the development of libraries from experimental data is discussed.


Characterizing (bio-)Macromolecules Using Hyphenated and Comprehensively Coupled Gas Chromatography-Based Techniques

Polymers are important materials in modern life. Synthetic polymers are used for clothing, to provide housing and shelter, for packaging materials, biomedical implants etc.


MS Solutions #13: NIST 11: What’s New and What Value Does it Offer? Part 3

The previous two installments provided information on the NIST/EPA/NIH Mass Spectral Database, past and present, and on the use of the NIST MS Search Program in identifying a compound from its mass spectrum using both the NIST EI Database and the NIST Database of spectra obtained using MS/MS techniques. In Part 3, the use of the searches in the Other Search tab view is examined. These searches can be beneficial to the identity of compounds from mass spectra obtained by ionization techniques other than EI and from data that provides a higher accuracy of the measure m/z value than is usually available for EI data.


MS Solutions #24: Choose the Right Interface for LC/MS Success

Many analysts that I speak with during training classes never consider anything beyond the electrospray interface for LC/MS. Electrospray is undeniably a very flexible technique.


MS Solutions #25: Ion Mobility Spectrometry: A Primer

Ion mobility spectrometry (IMS), by itself has found a niche in many areas including security screening, enviornmental monitoring, military applications, and analytical laboratory use.  The technique is not mass spectrometry, however it is related to MS by the fact that IMS does perform separation of ions.