This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and defini- tions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy's Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some addi- tional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, par- ticularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrom- etry terminology that represents the current consensus of the mass spectrometry community.

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Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013)

Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics.

Gas-phase chemistry of collisionally activated ions

Excessive oxidative stress leaves a protein carbonylation fingerprint in biological systems. Carbonylation is an irreversible post-translational modification (PTM) that often leads to the loss of protein function and can be a component of multiple diseases. Protein carbonyl groups can be generated directly (by amino acids oxidation and the α-amidation pathway) or indirectly by forming adducts with lipid peroxidation products or glycation and advanced glycation end-products. Studies of oxidative stress are complicated by the low concentration of oxidation products and a wide array of routes by which proteins are carbonylated. The development of new selection and enrichment techniques coupled with advances in mass spectrometry are allowing the identification of hundreds of new carbonylated protein products from a broad range of proteins located at many sites in biological systems. The focus of this review is on the use of proteomics tools and methods to identify oxidized proteins along with specific sites o...

Proteomic identification of carbonylated proteins and their oxidation sites.

Background: Although robust discovery-phase platforms have resulted in the generation of large numbers of candidate cancer biomarkers, a comparable system for subsequent quantitative assessment and verification of all candidates is lacking. Established immunoassays and available antibodies permit analysis of small subsets of candidates; however, the lack of commercially available reagents, coupled with high costs and lengthy production and purification times, have rendered the large majority of candidates untestable.

Content: Mass spectrometry (MS), and in particular multiple reaction monitoring (MRM)-MS, has emerged as an alternative technology to immunoassays for quantification of target proteins. Novel biomarkers are expected to be present in serum in the low (μg/L–ng/L) range, but analysis of complex serum or plasma digests by MS has yielded milligram per liter limits of detection at best. The coupling of prior sample purification strategies such as enrichment of target analytes, depletion of high-abundance proteins, and prefractionation, has enabled reliable penetration into the low microgram per liter range. This review highlights prospects for candidate verification through MS-based methods. We first outline the biomarker discovery pipeline and its existing bottleneck; we then discuss various MRM-based strategies for targeted protein quantification, the applicability of such methods for candidate verification, and points of concern.

Summary: Although it is unlikely that MS-based protein quantification will replace immunoassays in the near future, with the expected improvements in limits of detection and specificity in instrumentation, MRM-based approaches show great promise for alleviating the existing bottleneck to discovery.

/pdf/the-bottleneck-in-the-cancer-biomarker-pipeline-and-protein-10ylb1hiio.pdf

The Bottleneck in the Cancer Biomarker Pipeline and Protein Quantification through Mass Spectrometry–Based Approaches: Current Strategies for Candidate Verification

Procedures are developed in which the reversed-sector double-focusing mass spectrometer is employed to monitor signals due to specified ionic reactions. These procedures are employed to determine chlorine isotope effects for positive and negative ions fragmenting both unimolecularly and on collision at high velocity. Values of the /sup 35/Cl//sup 37/Cl isotope effect are measured for reactions involving Cl. and HCl elimination and are found to range from unity to 1.2. A dependence is noted upon the internal energy of the ion and, in the case of chlorobenzenes, on the nature of the para substituent. Fragmentations of positive ions which are subject only to secondary chlorine isotope effects are monitored to provide internal standards and as a check upon possible isotope effects in the chemical ionization source. The magnitudes of the kinetic heavy atom isotope effects for positive ions are rationalized in terms of the strength of the C--Cl bond as determined chiefly by the contribution of the chloronium (>C=Cl/sup +/) resonance form. A value of 1.19 +- 0.01 (95% confidence) is recorded as the secondary chlorine isotope effect for HCl elimination from the negative ions formed by chloride ion attachment to benzoic acid. The error in this determination is no moremore » than 5%. 2 tables, 2 figures.« less

Chlorine isotope effects in mass spectrometry by multiple reaction monitoring

Selected fragment scans of mass spectrometers in direct mixture analysis

Particular nitrogen-containing compounds, in some cases individual isomers, can be identified in coal liquid samples by mass-analyzed ion kinetic energy spectrometry (MIKES). This is done directly, without prior treatment or fractionation of the sample. Isobutane chemical ionization (CI) is employed to give an approximate molecular weight profile of the coal liquid. Nitrogen-containing ions are recognized by their enhanced tendency for charge stripping as evident in E/2 mass spectra or by using ammonia as the CI reagent. In selected cases, comparison with authentic compounds has been used to verify the MIKES identifications.

Analysis of coal liquids by mass-analyzed ion kinetic energy spectrometry

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Chlorine isotope effects in mass spectrometry by multiple reaction monitoring

Selected fragment scans of mass spectrometers in direct mixture analysis

Analysis of coal liquids by mass-analyzed ion kinetic energy spectrometry