Although direct fragmentation of protein ions in a mass spectrometer is far more efficient than exhaustive mapping of 1-3 kDa peptides for complete characterization of primary structures predicted from sequenced genomes, the development of this approach is still in its infancy. Here we describe a statistical model (good to within approximately 5%) that shows that the database search specificity of this method requires only three of four fragment ions to match (at +/-0.1 Da) for a 99.8% probability of being correct in a database of 5,000 protein forms. Software developed for automated processing of protein ion fragmentation data and for probability-based retrieval of whole proteins is illustrated by identification of 18 archaeal and bacterial proteins with simultaneous mass-spectrometric (MS) mapping of their entire primary structures. Dissociation of two or three proteins at once for such identifications in parallel is also demonstrated, along with retention and exact localization of a phosphorylated serine residue through the fragmentation process. These conceptual and technical advances should assist future processing of whole proteins in a higher throughput format for more robust detection of co- and post-translational modifications.

A significant challenge to understanding dynamic and heterogeneous brain systems lies in the chemical complexity of secreted intercellular messengers that change rapidly with space and time. Two solid-phase extraction collection strategies are presented that relate time and location of peptide release with mass spectrometric characterization. Here, complex suites of peptide-based cell-to-cell signaling molecules are characterized from the mammalian suprachiasmatic nucleus (SCN), site of the master circadian clock. Observed SCN releasates are peptide rich and demonstrate the corelease of established circadian neuropeptides and peptides with unknown roles in circadian rhythms. Additionally, the content of SCN releasate is stimulation specific. Stimulation paradigms reported to alter clock timing, including electrical stimulation of the retinohypothalamic tract, produce releasate mass spectra that are notably different from the spectra of compounds secreted endogenously over the course of the 24-h cycle. In addition to established SCN peptides, we report the presence of proSAAS peptides in releasates. One of these peptides, little SAAS, exhibits robust retinohypothalamic tract-stimulated release from the SCN, and exogenous application of little SAAS induces a phase delay consistent with light-mediated cues regulating circadian timing. These mass spectrometry-based analyses provide a new perspective on peptidergic signaling within the SCN and demonstrate that the integration of secreted compounds with information relating time and location of release generates new insights into intercellular signaling in the brain.little SAAS ͉ neuropeptides ͉ solid-phase extraction ͉ peptidomics ͉ suprachiasmatic nucleus A fundamental component of cell-to-cell signaling in the brain is the release of endogenously derived neuropeptidebased transmitters and modulators within dynamic neural networks. Neuropeptides include a broad set of structurally diverse molecules that are physiologically active at low concentrations and localize across heterogeneous brain regions, particularly throughout neuroendocrine systems. These properties contribute marked chemical complexity to neurotransmission within heterogeneous and dynamic brain systems. Directly acquiring releasate information about chemical content, release site distribution, and stimulation dependence is a significant challenge to the study of neuronal networks incorporating neuropeptide intercellular signaling.This article describes the use of several unique peptide sampling approaches to characterize chemically complex releasates from the rat suprachiasmatic nucleus (SCN), the site of the master circadian clock (1, 2). The SCN is highly innervated with peptidergic efferents, afferents, and interneurons (3). Moreover, SCN humoral signals are critical elements for the coordination of biological rhythms because SCN transplants can restore aspects of circadian rhythms in SCN-ablated animals (4). In the present work, SCN releasates were collected and concentrated directly from brain sl...

For the identification and characterization of proteins harboring posttranslational modifications (PTMs), a "top down" strategy using mass spectrometry has been forwarded recently but languishes without tailored software widely available. We describe a Web-based software and database suite called ProSight PTM constructed for large-scale proteome projects involving direct fragmentation of intact protein ions. Four main components of ProSight PTM are a database retrieval algorithm (Retriever), MySQL protein databases, a file/data manager, and a project tracker. Retriever performs probability-based identifications from absolute fragment ion masses, automatically compiled sequence tags, or a combination of the two, with graphical rendering and browsing of the results. The database structure allows known and putative protein forms to be searched, with prior or predicted PTM knowledge used during each search. Initial functionality is illustrated with a 36-kDa yeast protein identified from a processed cell extract after automated data acquisition using a quadrupole-FT hybrid mass spectrometer. A +142-Da delta(m) on glyceraldehyde-3-phosphate dehydrogenase was automatically localized between Asp90 and Asp192, consistent with its two cystine residues (149 and 153) alkylated by acrylamide (+71 Da each) during the gel-based sample preparation. ProSight PTM is the first search engine and Web environment for identification of intact proteins (https://prosightptm.scs.uiuc.edu/).

The human proteome is a highly complex extension of the genome wherein a single gene often produces distinct protein forms due to alternative splicing, RNA editing, polymorphisms, and posttranslational modifications. Due to the presence of polymorphisms, alternative splicing, and posttranslational modifications (PTMs) 1 the human proteome is highly complex, often encoding multiple protein forms for a given gene (1). This biological complexity poses a significant analytical and bioinformatic challenge to the detailed analysis of mammalian proteomes by MS and is exacerbated by the presence of gene families sharing high sequence identity (2, 3). Protein modifications are often indicative of changes in cellular or tissue dynamics and therefore play central roles in regulation of the cell cycle or development of disease. Whether for new diagnostics or understanding molecular mechanisms in cell biology, protein identification using tryptic peptides has revolutionized the analysis of complex mixtures by mass spectrometry (1, 4). High throughput platforms based on MALDI (5) and ESI use MS/MS engines capable of spectral acquisition at a rate of Ͼ10 4 /week (6, 7). Recent studies indicate significant inefficiencies associated with such large scale "bottom up" analyses in mammalian systems including imperfect enzymatic cleavage (8, 9) and some MS/MS spectra requiring manual interpretation/validation for identification. Despite the lingering difficulties with peptide analysis, it provides the best and most general method for large scale protein identification today with information on nonsynonymous coding single nucleotide polymorphisms (cSNPs), alternative splicing (10), and PTMs challenging to obtain (2).Recent developments by MacCoss et al. (11), Wu et al. (12), and Zhu et al. (13) use three proteases and multidimensional protein identification technology ("MudPIT") or isoelectric focusing, reversed-phase chromatography, and three mass spectrometers (13), respectively, to obtain mass information on ϳ70 -99% of the primary protein structure. Combining intact protein measurement with near exhaustive peptide analysis of five proteins from human cells allowed detection of N-terminal modifications and one alternatively spliced transcript (13). Although cSNP analysis of abundant blood proteins is possible (14), a general informatic strategy has yet to systematically integrate DNA and RNA level data with the MS-based interrogation of the human proteome. This is accomplished here using a data base of human proteins tailored

For interrogation of peptides with diverse modifications, no other instrument is as versatile as the Fourier‐transform mass spectrometer (FTMS). Particularly using electrospray ionization (ESI), many intact proteins and their proteolytic products harboring post‐translational and chemical modifications (PTMs) have been studied by high resolution tandem mass spectrometry (MS/MS). The widely touted analytical figures of merit for FTMS in fact have translated into clarity when analyzing PTMs from phosphorylations to disulfides, oxidations, methylations, acetylations, and even exotic PTMs found in the biosynthesis of antibiotics and other natural products. A top down approach to PTM detection and localization is proving extensible to an increasing variety of PTMs, some of which are stable to MS/MS at the protein level but unstable to amide bond cleavage by threshold dissociations at the level of small peptides <3 kDa. In contrast, MS/MS using electron capture dissociation (ECD) allows precise localization of even labile PTMs given enough sample and abundant molecular ions. Finally, this brief synopsis of recent literature highlights specific PTMs that perturb the protein backbone therefore altering MS/MS fragmentation patterns. Thus, FTMS will continue its expansion into more laboratories in part because of its ability to detect and deconvolute the regulatory mechanisms of biology written in the language of PTMs. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:126–134, 2005