Evaluation of HCD- and CID-type Fragmentation Within Their Respective Detection Platforms For Murine Phosphoproteomics

Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Molecular & Cellular Proteomics (Impact Factor: 6.56). 09/2011; 10(12):M111.009910. DOI: 10.1074/mcp.M111.009910
Source: PubMed


Protein phosphorylation modulates a myriad of biological functions, and its regulation is vital for proper cellular activity. Mass spectrometry is the enabling tool for phosphopeptide analysis, where recent instrumentation advances in both speed and sensitivity in linear ion trap and orbitrap technologies may yield more comprehensive phosphoproteomic analyses in less time. Protein phosphorylation analysis by MS relies on structural information derived through controlled peptide fragmentation. Compared with traditional, ion-trap-based collision-induced dissociation (CID), a more recent type of fragmentation termed HCD (higher energy collisional dissociation) provides beam type CID tandem MS with detection of fragment ions at high resolution in the orbitrap mass analyzer. Here we compared HCD to traditional CID for large-scale phosphorylation analyses of murine brain under three separate experimental conditions. These included a same-precursor analysis where CID and HCD scans were performed back-to-back, separate analyses of a phosphotyrosine peptide immunoprecipitation experiment, and separate whole phosphoproteome analyses. HCD generally provided higher search engine scores with more peptides identified, thus out-performing CID for back-to-back experiments for most metrics tested. However, for phosphotyrosine IPs and in a full phosphoproteome study of mouse brain, the greater acquisition speed of CID-only analyses provided larger data sets. We reconciled our results with those in direct contradiction from Nagaraj N, D'Souza RCJ et al. (J. Proteome Res. 9:6786, 2010). We conclude, for large-scale phosphoproteomics, CID fragmentation with rapid detection in the ion trap still produced substantially richer data sets, but the back-to-back experiments demonstrated the promise of HCD and orbitrap detection for the future.

Download full-text


Available from: Edward L Huttlin, Nov 18, 2015
  • Source
    • "Only b and y ions were scored. Matched peptides were filtered by linear discriminant analysis to reduce peptide false discovery rate of <0.5%, based on numerous parameters including XCorr, ΔCn, precursor mass error, and charge state [30]. The confidence of each phosphopeptide site assignment was determined by the Ascore program [31]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive loss of cognitive function. One of the pathological hallmarks of AD is the formation of neurofibrillary tangles composed of abnormally hyperphosphorylated tau protein, but global deregulation of protein phosphorylation in AD is not well analyzed. Here we report a pilot investigation of AD phosphoproteome by titanium dioxide enrichment coupled with high resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). During the optimization of the enrichment method, we found that phosphate ion at a low concentration (e.g. 1 mM) worked efficiently as a non-phosphopeptide competitor to reduce background. The procedure was further tuned with respect to peptide-to-bead ratio, phosphopeptide recovery and purity. Using this refined method and 9 h LC-MS/MS, we analyzed phosphoproteome in one milligram of digested AD brain lysate, identifying 5243 phosphopeptides containing 3715 non-redundant phosphosites on 1455 proteins, including 31 phosphosites on the tau protein. This modified enrichment method is simple and highly efficient. The AD case study demonstrates its feasibility of dissecting phosphoproteome in a limited amount of postmortem human brain.This article is protected by copyright. All rights reserved
    Full-text · Article · Oct 2014 · Proteomics
  • Source
    • "We also explored a strategy to minimize the blood sample requirement as a means to facilitate repeat PK sampling, particularly in small animal models. This strategy involved quantitating hepcidin on a Orbitrap MS (Q-Exactive) (Michalski et al., 2011), which is capable of effectively fragmenting large peptides with rapidly detecting the entire MS/MS spectrum with high mass accuracy (Jedrychowski et al., 2011). The Q-Exactive has been reported to be successfully used in targeted proteomic quantitation and PK/PD study for small molecules (Gallien et al., 2012; Knych, Casbeer, McKemie, & Arthur, 2013; Mélard et al., 2013; Zimmerlin & Kiffe, 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Introduction: A requisite step in developing a therapeutic to modulate the levels of hepcidin is the development of a quantitative method for measuring the concentration of serum hepcidin. Methods: To this end, an LC-MS method, based on selected reaction monitoring (SRM) with a triple quadrupole MS and an isotopically labeled hepcidin as internal standard, was developed to measure hepcidin in mouse and monkey sera. Results: Initially, 40 normal cynomolgus monkeys and 40 normal mice were studied to determine the normal endogenous levels of hepcidin, and an average of 50ng/mL was found in the monkeys and 46ng/mL in the mice. Next, experiments were conducted where an siRNA, targeting hepcidin, was administered to cynomolgus monkeys, resulting in effective hepcidin reduction (inhibition rate) of 87% after 24h and 74% after 48h, demonstrating to effectively reduce serume level of hepcidin. Conclusions: For better sensitivity, especially for the low volumes available for mouse sera, a second LC-MS method, based on parallel reaction monitoring (PRM) using a Orbitrap MS was developed and shown to be at least 10 fold lower in detection limits (or consumption of serum volume) than the SRM approach.
    Full-text · Article · Oct 2014 · Journal of Pharmacological and Toxicological Methods
  • Source
    • "For each mTRAQ experiment, we also combined CID and HCD data to derive a set of unique phosphopeptides. In addition to providing quantitative information (via mTRAQ reporter ions), HCD fragmentation also gave a significant number of unique phosphopeptides [30]. As a result, however, the amount of material available for each condition (pregnancy and non-pregnancy) was limited to approximately 100 μg according to the manufacturer’s protocol (see Materials and methods for details), resulting in a total of approximately 400 μg of labeled peptides after pooling the two samples into a single mTRAQ set. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnant and non-pregnant patients using gel electrophoresis and high-resolution mass spectrometry. Furthermore, we also apply a non-prefractionation quantitative phosphoproteomic approach using mTRAQ labeling to evaluate the expression of specific phosphoproteins during pregnancy comparison with non-pregnancy. In total, 2579 proteins (10429 unique peptides) were identified, including 1408 from the urine of pregnant volunteers and 1985 from the urine of non-pregnant volunteers. One thousand and twenty-three proteins were not reported in previous studies at the proteome level and were unique to our study. Furthermore, we obtained 237 phosphopeptides, representing 105 phosphoproteins. Among these phosphoproteins, 16 of them were found to be significantly differentially expressed, of which 14 were up-regulated and two were down-regulated in urine samples from women just before vaginal delivery. Taken together, these results offer a comprehensive urinary proteomic profile of healthy women during before and after vaginal delivery and novel information on the phosphoproteins that are differentially regulated during the maintenance of normal pregnancy. Our results may provide a better understanding of the mechanisms of pregnancy maintenance, potentially leading to the development of biomarker-based sensitive assays for understanding pregnancy.
    Full-text · Article · Nov 2013 · BMC Genomics
Show more