https://link.springer.com/content/pdf/10.1016/1044-0305(94)80016-2.pdf

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

https://cseweb.ucsd.edu/classes/sp10/cse283/notes/silac.pdf

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

Polydopamine and Its Derivative Materials: Synthesis and Promising Applications in Energy, Environmental, and Biomedical Fields

This book is written as a reference on organic substances in natural waters and as a supplementary text for graduate students in water chemistry. The chapters address five topics: amount, origin, nature, geochemistry, and characterization of organic carbon. Of these topics, the main themes are the amount and nature of dissolved organic carbon in natural waters (mainly fresh water, although seawater is briefly discussed). It is hoped that the reader is familiar with organic chemistry, but it is not necessary. The first part of the book is a general overview of the amount and general nature of dissolved organic carbon. Over the past 10 years there has been an exponential increase in knowledge on organic substances in water, which is the result of money directed toward the research of organic compounds, of new methods of analysis (such as gas chromatography and mass spectrometry), and most importantly, the result of more people working in this field. Because of this exponential increase in knowledge, there is a need to pull together and summarize the data that has accumulated from many disciplines over the last decade.

Organic geochemistry of natural waters

A summary of the ion types observed in the Fast Atom Bombardment Mass Spectrometry (FAB-MS) and collision induced decomposition (CID) MS/MS spectra of glycoconjugates (glycosphingolipids, glycopeptides, glycosides and carbohydrates) is presented. The variety of product ion types that arise by cleavages within the carbohydrate moieties has prompted us to introduce a systematic nomenclature to designate these ions. The proposed nomenclature has been developed primarily for FAB-MS, but can be used as well for other ionization techniques [field desorption (FD), direct chemical ionization (DCI), laser desorption/Fourier transform (LD/FT), etc.], and is applicable to spectra recorded in either the positive or negative ion mode during both MS and MS/MS experiments. Ai, Bi and Ci labels are used to designate fragments containing a terminal (nonreducing end) sugar unit, whereas Xj, Yj and Zj represent ions still containing the aglycone (or the reducing sugar unit). Subscripts indicate the position relative to the termini analogous to the system used in peptides, and superscripts indicate cleavages within carbohydrate rings. FAB-MS/MS spectra of a native glycosphingolipid and glycopeptide, and a permethylated ganglioside are shown as illustrations.

A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates

With the advent of recombinant deoxyribonucleic acid (DNA) technology which allows a wide range of manipulation of genes and their expression in cell lines other than the natural ones, many aspects of protein structure have become more important than ever. In addition to the determination of the amino acid sequence questions relating to homogeneity, the nature of post-translational modifications, the verification of the structure of a protein produced by a synthetically modified gene or the detection of a natural mutant are all questions that are more and more frequently asked and with the demand for more detail. Mass spectrometry has emerged as an important contributor to this field, particularly since the advent of fast atom bombardment (FAB) ionization, which makes it possible to ionize directly large polar molecules such as peptides and small proteins. As such, FAB mass spectrometry provides mainly molecular weight information which, in itself, often sufficies to answer certain questions, particularly because the mass of many peptides can be determined directly from a single mass spectrum of a mixture. However, in order to obtain detailed structural information, such as the amino acid sequence, fragmentation has to be induced by collision processes and the product ions separated, preferably in the second mass spectrometer of a tandem system. This approach is particularly suited for the determination of the sequence of N-blocked peptides and the nature of the blocking group; the type and location of modified (i.e. phosphorylated, sulfated, glycosylated) amino acids; detection or verification of amino acid replacements; confirmation of the structure of synthetic peptides; and last but not least, the determination of the primary structure of proteins.

Contributions of mass spectrometry to peptide and protein structure.

Mass spectrometric determination of the amino acid sequence of peptides and proteins

A total of four Martian samples, one surface and one subsurface sample at each of the two Viking landing sites, Chryse Planitia and Utopia Planitia, have been analyzed for organic compounds by a gas chromatograph-mass spectrometer. In none of these experiments could organic material of Martian origin be detected at detection limits generally of the order of parts per billion and for a few substances closer to parts per million. The evolution of water and carbon dioxide, but not of other inorganic gases, was observed upon heating the sample to temperatures of up to 500 C. The absence of organic compounds seems to preclude their production on the planet at rates that exceed the rate of their destruction. It also makes it unlikely that living systems that behave in a manner similar to terrestrial biota exist, at least at the two Viking landing sites.

Klaus Biemann

Papers

Contributions of mass spectrometry to peptide and protein structure.

Mass spectrometric determination of the amino acid sequence of peptides and proteins

The search for organic substances and inorganic volatile compounds in the surface of Mars

Collision-induced fragmentation of (M + H)+ ions of peptides. Side chain specific sequence ions

Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine.