Overview of Peptide and Protein Analysis by Mass Spectrometry

Abstract

One goal of this introductory overview is to try and dispel the still widely held, but now mistaken, belief that mass spectrometry is beyond the technical resources of the typical laboratory or facility engaged in the structural characterization or synthesis of peptides and proteins. Over the last five years, mass spectrometers and associated data systems have become available that can be operated by anyone capable of running a modern amino acid analyzer or Edman sequencer, yet are powerful enough to handle the most demanding analyses that the peptide or protein investigator might require. The remaining goals of this article are to familiarize peptide and protein chemists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide. The emphasis here is on established tools and techniques that can realistically be used for problem solving. As a result, many useful instruments and techniques employed by the trained mass spectroscopist are not discussed here, because they do not satisfy these criteria or are not yet widely available; however, a few of these are briefly mentioned at the end of the unit. The overview concludes with a tutorial discussion on the meaning and practical importance of a number of fundamental experimental and performance-related issues that have important implications for interpretation and use of mass spectral data, such as mass accuracy and resolution.

Optimization of titanium dioxide and immunoaffinity-based enrichment procedures for tyrosine phosphopeptide using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

“…MALDI-TOF MS has been used primarily for rapid and robust analysis of phosphopeptide enrichment because it is suitable for relatively simple standard mixtures and enables the preparation of multiple samples simultaneously [48]. In contrast, LC-MS analysis is a relatively slow and very sensitive technique in which the mixture of peptides is separated by an LC gradient, and each peptide is analyzed in solution by LC-MS. LC-MS analysis is suitable for complex mixtures of peptides.…”

Targeted Degradation of Proteins by PROTACs

“…Confirm the identity of the fully assembled PROTAC using electrospray ionization mass spectrometry (ESI-MS; see, e.g., Carr and Annan, 1996). Confirm the identity of the fully assembled PROTAC using electrospray ionization mass spectrometry (ESI-MS; see, e.g., Carr and Annan, 1996).…”

Synthesis and Application of Interstrand Cross‐Linked Duplexes by Covalently Linking a Pair of Abasic Sites

“…(Aminooxy)acetic acid hemihydrochloride (1) Additional reagents and equipment for TLC (Meyers, 2000a), column chromatography (Meyers, 2000b), H 1 and C 13 NMR (James, 2000), and mass spectrometry (Carr & Annan, 1996) Preparation of (N-tritylaminooxy)acetic acid ( 15 H,Tr),4.11 (s,2 H,CH 2 (br s,2 H,NH),8.36 (br s,2 H,NH),4 H,naph),7.52 (t,2 H,naph,J = 7.9 Hz),30 H,Tr),4.23 (s,4 H,CH 2…”

“…Current Protocols in Nucleic Acid Chemistry Additional reagents and equipment for reversed-phase HPLC (Ellington & Pollard, 2000) and mass spectrometry (Carr & Annan, 1996) UDG reaction 1. In a 1.5-mL microcentrifuge tube, dissolve 2.52 nmol purified ODN-I and 2.52 nmol of the complementary ODN-II in 99.0 μL UDG reaction buffer.…”