Skip to main content
 

MS Solutions

 
 
 
 
 

MS Solutions

MS Solutions #28: Quality: The Third Side of the Analytical Success Triangle

As analytical chemists, we spend considerable time thinking about and working with basic scientific principles combined with the technology and products that allow us to solve our analytical problems. However, it is essential for success of any method and for the long-term success of a laboratory operation that our science and technology are supported by a quality system that ensures continuing achievement of our operational goals. We therefore present a triangle concept for analytical success: One side of the triangle shows our need to understand fundamental scientific concepts. A second, and equally sized side, is the ability to apply current technology, applications, software, and techniques in the laboratory. Finally, the base of this equilateral triangle is the quality system. If any one side of the triangle is given inadequate attention or, worse yet, is missing then we cannot hope to achieve overall success for the laboratory operation.

 

MS Solutions #27: The Importance of the Limits Option in the NIST Mass Spectral Search Program Especially When Used with the Wiley Registry of Mass Spectral Data

Over the last several editions, starting with at least the 6th edition, the Wiley Registry of Mass Spectral Data has contained a number of “single-peak” spectra such as those shown in Figure 1. Such spectra in an EI database used for the identification of unknowns based on their mass spectra are of no benefit.

 

MS Solutions #26: FAIMS/DMS Applications Overview

In last month’s edition of MS Solutions I described the technology behind Field Asymmetric Ion Mobility Spectrometry (FAIMS), also known as Differential Mobility Spectrometry (DMS). In that article we learned that ions of identical m/z value may be separated in a FAIMS/DMS device based on their mobility differences in a high potential electrical field. In this month’s article we are going to look at the incorporation of FAIMS/DMS into a conventional LC/MS system to provide an added dimension of ion separation which is orthogonal to both chromatographic and mass spectrometric separation mechanisms.

 

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.

 

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 #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.

 

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 #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.  

 

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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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.

 

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.

 

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.

 

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 #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

 

MS Solutions #26: FAIMS/DMS Applications Overview

In last month’s edition of MS Solutions I described the technology behind Field Asymmetric Ion Mobility Spectrometry (FAIMS), also known as Differential Mobility Spectrometry (DMS). In that article we learned that ions of identical m/z value may be separated in a FAIMS/DMS device based on their mobility differences in a high potential electrical field. In this month’s article we are going to look at the incorporation of FAIMS/DMS into a conventional LC/MS system to provide an added dimension of ion separation which is orthogonal to both chromatographic and mass spectrometric separation mechanisms.

 

MS Solutions #28: Quality: The Third Side of the Analytical Success Triangle

As analytical chemists, we spend considerable time thinking about and working with basic scientific principles combined with the technology and products that allow us to solve our analytical problems. However, it is essential for success of any method and for the long-term success of a laboratory operation that our science and technology are supported by a quality system that ensures continuing achievement of our operational goals. We therefore present a triangle concept for analytical success: One side of the triangle shows our need to understand fundamental scientific concepts. A second, and equally sized side, is the ability to apply current technology, applications, software, and techniques in the laboratory. Finally, the base of this equilateral triangle is the quality system. If any one side of the triangle is given inadequate attention or, worse yet, is missing then we cannot hope to achieve overall success for the laboratory operation.

 

MS Solutions #27: The Importance of the Limits Option in the NIST Mass Spectral Search Program Especially When Used with the Wiley Registry of Mass Spectral Data

Over the last several editions, starting with at least the 6th edition, the Wiley Registry of Mass Spectral Data has contained a number of “single-peak” spectra such as those shown in Figure 1. Such spectra in an EI database used for the identification of unknowns based on their mass spectra are of no benefit.