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1.  Human SRMAtlas: A resource of targeted assays to quantify the complete human proteome 
Cell  2016;166(3):766-778.
Summary
The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell-type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive and robust targeted mass spectrometric method selected reaction monitoring, SRM. This human SRMAtlas provides definitive coordinates that conclusively identify the respective peptide in biological samples. We report data on 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations and post-translational modifications. The data is freely accessible as a resource at www.srmatlas.org, and we demonstrate its utility by examining the network response to inhibition of cholesterol synthesis in liver cells and to docetaxel in prostate cancer lines.
doi:10.1016/j.cell.2016.06.041
PMCID: PMC5245710  PMID: 27453469
2.  Proteomic response of methicillin-resistant S. aureus to a synergistic antibacterial drug combination: a novel erythromycin derivative and oxacillin 
Scientific Reports  2016;6:19841.
The use of antibacterial drug combinations with synergistic effects is increasingly seen as a critical strategy to combat multi-drug resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). In this work, the proteome responses in MRSA under the stress of a sub-inhibitory dose of a synergistic drug combination of a novel erythromycin derivative, SIPI-8294, and oxacillin, were studied by label-free quantitative proteomics. Several control treatment groups were designed to isolate proteome responses potentially related to the synergy: (1) the non-synergistic drug combination of erythromycin and oxacillin, (2) SIPI-8294 only, (3) oxacillin only and (4) erythromycin only. Results showed that 200 proteins were differentially expressed in SIPI-8294/oxacillin-treated cells. Among these proteins, the level of penicillin binding protein 2a, the protein mainly responsible for oxacillin resistance in MRSA, was four times lower in the SIPI-8294/oxacillin group than in the erythromycin/oxacillin group, suggesting that SIPI-8294 may interfere with this known oxacillin resistance mechanism. Moreover, hierarchical clustering analysis of differentially expressed proteins under different treatments revealed that SIPI-8294/oxacillin elicits very different responses than the individual drugs or the non-synergistic erythromycin/oxacillin combination. Bioinformatic analysis indicated that the synergistic effect can be further traced to a disruption in oxidation-reduction homeostasis and cell wall biosynthesis.
doi:10.1038/srep19841
PMCID: PMC4726183  PMID: 26806358
3.  The Use of Nipple Shields: A Review 
Introduction
A nipple shield is a breastfeeding aid with a nipple-shaped shield that is positioned over the nipple and areola prior to nursing. Nipple shields are usually recommended to mothers with flat nipples or in cases in which there is a failure of the baby to effectively latch onto the breast within the first 2 days postpartum. The use of nipple shields is a controversial topic in the field of lactation. Its use has been an issue in the clinical literature since some older studies discovered reduced breast milk transfer when using nipple shields, while more recent studies reported successful breastfeeding outcomes. The purpose of this review was to examine the evidence and outcomes associated with nipple shield use.
Methods
A literature search was conducted in Ovid MEDLINE, OLDMEDLINE, EMBASE Classic, EMBASE, Cochrane Central Register of Controlled Trials, and CINAHL. The primary endpoint was any breastfeeding outcome following nipple shield use. Secondary endpoints included the reasons for nipple shield use and the average/median length of use. For the analysis, we examined the effect of nipple shield use on physiological responses, premature infants, mothers’ experiences, and health professionals’ experiences.
Results
The literature search yielded 261 articles, 14 of which were included in this review. Of these 14 articles, three reported on physiological responses, two reported on premature infants, eight reported on mothers’ experiences, and one reported on health professionals’ experiences.
Conclusion
Through examining the use of nipple shields, further insight is provided on the advantages and disadvantages of this practice, thus allowing clinicians and researchers to address improvements on areas that will benefit mothers and infants the most.
doi:10.3389/fpubh.2015.00236
PMCID: PMC4607874  PMID: 26528467
nipple shield; breastfeeding; lactation
4.  A Selected Review of the Mortality Rates of Neonatal Intensive Care Units 
Introduction
Newborn babies in need of critical medical attention are normally admitted to the neonatal intensive care unit (NICU). These infants tend to be preterm, have low birth weight, and/or have serious medical conditions. Neonatal survival varies, but progress in perinatal and neonatal care has notably diminished mortality rates. In this selected review, we examine and compare the NICU mortality rates and etiologies of death in different countries.
Methods
A literature search was conducted in Ovid MEDLINE, OLDMEDLINE, EMBASE Classic, and EMBASE. The primary endpoint was the mortality rates in NICUs. Secondary endpoints included the reasons for death and the correlation between infant age and mortality outcome. For the main analysis, we examined all infants admitted to NICUs. Subgroup analyses included extremely low birth weight infants (based on the authors’ own definition), very low birth weight infants, very preterm infants, preterm infants, preterm infants with a birth weight of ≤1,500 g, and by developed and developing countries.
Results
The literature search yielded 1,865 articles, of which 20 were included. The total mortality rates greatly varied among countries. Infants in developed and developing countries had similar ages at death, ranging from 4 to 20 days and 1 to 28.9 days, respectively. The mortality rates ranged from 4 to 46% in developed countries and 0.2 to 64.4% in developing countries.
Conclusion
The mortality rates of NICUs vary between nations but remain high in both developing and developed countries.
doi:10.3389/fpubh.2015.00225
PMCID: PMC4595739  PMID: 26501049
neonatal intensive care unit; mortality rate; prematurity
5.  A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation 
Scientific Reports  2015;5:14337.
Shotgun proteomics is an emerging tool for bacterial identification and differentiation. However, the identification of the mass spectra of peptides to genome-derived peptide sequences remains a key issue that limits the use of shotgun proteomics to bacteria with genome sequences available. In this proof-of-concept study, we report a novel bacterial fingerprinting method that enjoys the resolving power and accuracy of mass spectrometry without the burden of peptide identification (i.e. genome sequence-independent). This method uses a similarity-clustering algorithm to search for mass spectra that are derived from the same peptide and merge them into a unique consensus spectrum as the basis to generate proteomic fingerprints of bacterial isolates. In comparison to a traditional peptide identification-based shotgun proteomics workflow and a PCR-based DNA fingerprinting method targeting the repetitive extragenic palindromes elements in bacterial genomes, the novel method generated fingerprints that were richer in information and more discriminative in differentiating E. coli isolates by their animal sources. The novel method is readily deployable to any cultivable bacteria, and may be used for several fields of study such as environmental microbiology, applied microbiology, and clinical microbiology.
doi:10.1038/srep14337
PMCID: PMC4585814  PMID: 26395646
6.  An open-source computational and data resource to analyze digital maps of immunopeptidomes 
eLife  null;4:e07661.
We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.
DOI: http://dx.doi.org/10.7554/eLife.07661.001
eLife digest
The cells of the immune system protect us by recognizing telltale molecules produced by damaged and diseased cells, or by infection-causing microorganisms (which are also called pathogens). To help with this process, the cells in our bodies display small fragments of proteins (called peptides) on their surface that are then checked by the immune cells. Collectively, these peptides are referred to as the ‘immunopeptidome’, and deciphering the complexity of the human immunopeptidome is important for both basic research and medical science. Such an achievement would help to guide the development of next-generation vaccines and therapies against autoimmune disorders, infectious diseases and cancers.
In the past, immune peptides were mostly identified using a technique that is commonly called ‘shotgun’ mass spectrometry. However, this approach doesn't always provide reproducible results. In 2012, researchers reported the development of a new approach—which they called ‘SWATH’ mass spectrometry—that could yield more reproducible data.
Now, Caron et al.—including many of the researchers involved in the 2012 study—have developed a large collection of standardized tests that use SWATH mass spectrometry to analyze the human immunopeptidome. The workflow and the computational and data resources developed as part of this international effort are the first steps toward highly reproducible and measurable analyses of the immunopeptidome across many samples. Moreover, the large repository of assays generated by the project has been made public and will serve a large community of researchers, which should enable better collaborations.
In the future, SWATH mass spectrometry could be used as a robust technology for the reproducible detection and measurement of pathogen-specific or cancer-specific immune peptides. This could greatly help in the design of personalized immune-based therapies.
DOI: http://dx.doi.org/10.7554/eLife.07661.002
doi:10.7554/eLife.07661
PMCID: PMC4507788  PMID: 26154972
human leukocytes antigen; immunopeptidome; targeted mass spectrometry; SWATH-MS; DIA; human
7.  A draft map of the human proteome 
Kim, Min-Sik | Pinto, Sneha M. | Getnet, Derese | Nirujogi, Raja Sekhar | Manda, Srikanth S. | Chaerkady, Raghothama | Madugundu, Anil K. | Kelkar, Dhanashree S. | Isserlin, Ruth | Jain, Shobhit | Thomas, Joji K. | Muthusamy, Babylakshmi | Leal-Rojas, Pamela | Kumar, Praveen | Sahasrabuddhe, Nandini A. | Balakrishnan, Lavanya | Advani, Jayshree | George, Bijesh | Renuse, Santosh | Selvan, Lakshmi Dhevi N. | Patil, Arun H. | Nanjappa, Vishalakshi | Radhakrishnan, Aneesha | Prasad, Samarjeet | Subbannayya, Tejaswini | Raju, Rajesh | Kumar, Manish | Sreenivasamurthy, Sreelakshmi K. | Marimuthu, Arivusudar | Sathe, Gajanan J. | Chavan, Sandip | Datta, Keshava K. | Subbannayya, Yashwanth | Sahu, Apeksha | Yelamanchi, Soujanya D. | Jayaram, Savita | Rajagopalan, Pavithra | Sharma, Jyoti | Murthy, Krishna R. | Syed, Nazia | Goel, Renu | Khan, Aafaque A. | Ahmad, Sartaj | Dey, Gourav | Mudgal, Keshav | Chatterjee, Aditi | Huang, Tai-Chung | Zhong, Jun | Wu, Xinyan | Shaw, Patrick G. | Freed, Donald | Zahari, Muhammad S. | Mukherjee, Kanchan K. | Shankar, Subramanian | Mahadevan, Anita | Lam, Henry | Mitchell, Christopher J. | Shankar, Susarla Krishna | Satishchandra, Parthasarathy | Schroeder, John T. | Sirdeshmukh, Ravi | Maitra, Anirban | Leach, Steven D. | Drake, Charles G. | Halushka, Marc K. | Prasad, T. S. Keshava | Hruban, Ralph H. | Kerr, Candace L. | Bader, Gary D. | Iacobuzio-Donahue, Christine A. | Gowda, Harsha | Pandey, Akhilesh
Nature  2014;509(7502):575-581.
The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here, we present a draft map of the human proteome using high resolution Fourier transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells resulted in identification of proteins encoded by 17,294 genes accounting for ~84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream ORFs. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.
doi:10.1038/nature13302
PMCID: PMC4403737  PMID: 24870542
8.  Use of urinary markers in cancer setting: A literature review 
Journal of Bone Oncology  2015;4(1):18-23.
Introduction
In bone metastases, the disruption of normal bone processes results in increased resorption and formation rates, which can often be quantitatively measured by biomarkers in the urine and blood. The purpose of this review is to summarize relevant studies of urinary markers used as a diagnostic and/or prognostic tool, as well as its potential and advances in directing therapy.
Methods
A literature search was conducted using Ovid MEDLINE (1950 to July 2014), EMBASE (1950 to 2014 week 30) and Cochrane Central Register of Controlled Trials (3rd Quarter 2014) to identify studies that detailed the use of urinary markers in the cancer setting, specifically involving markers for bone metastases. Search terms included “urinary markers”, “cancer”, and “bone metastases”.
Results
A total of 35 articles, with 24 original studies, were identified. In general, urinary markers can be used to detect early signs of bone metastases prior to skeletal imaging, but still must be used in conjunction with imaging to avoid false positive results. The use of urinary markers, such as N-telopeptide, as a prognostic tool remains controversial, but can provide information on the relative risk of skeletal related events (SREs), disease progression, as well as death. Finally, while urinary markers have shown to be potentially useful in confirming the efficacy of bone metastases treatments, exploring the appropriate dosages for treatment, and directing therapy, it is still unclear to what extent urinary markers should be reduced by.
Conclusion
The potential use of urinary markers in the management of bone metastases is promising as it can allow for earlier and more convenient detection of bone metastases in comparison to other techniques. However, additional studies involving prospective clinical trials are suggested to further examine the potential of urinary markers in developing appropriate treatment strategies and endpoints, especially in developing a clearer protocol on the extent urinary markers should be reduced by to correlate with achievement of clinical benefit.
doi:10.1016/j.jbo.2015.01.002
PMCID: PMC4620969  PMID: 26579485
Urinary markers; Bone metastases; Cancer; Diagnostic use; Prognostic use; Directing therapy
9.  Quality of life after palliative radiotherapy in bone metastases: A literature review 
Journal of Bone Oncology  2014;4(1):24-31.
Objective
To investigate the quality of life (QOL) following palliative radiotherapy for painful bone metastases.
Methods
A literature search was conducted in OvidSP Medline (1946–Jan Week 4 2014), Embase (1947–Week 5 2014), and the Cochrane Central Register of Controlled Trials (Dec 2013) databases. The search was limited to English. Subject headings and keywords included ‘palliative radiation’, ‘cancer palliative therapy’, ‘bone metastases’, ‘quality of life’, and ‘pain’. All studies (prospective or retrospective) reporting change in QOL before and after palliative radiotherapy for painful bone metastases were included.
Results
Eighteen articles were selected from a total of 1730. The most commonly used tool to evaluate QOL was the Brief Pain Inventory. Seventeen studies collected data prospectively. An improvement in symptoms and functional interference scores following radiotherapy was observed in all studies. The difference in changes in QOL between responders and non responders was inconsistently reported.
Conclusion
QOL improves in patients who respond to palliative radiotherapy for painful bone metastases.
doi:10.1016/j.jbo.2014.11.001
PMCID: PMC4620945  PMID: 26579481
Quality of life; Radiation therapy; Bone metastases; Advanced cancer
10.  International patterns of practice in radiotherapy for bone metastases: A review of the literature 
Journal of Bone Oncology  2014;3(3-4):96-102.
Purpose: Radiation therapy is the standard treatment for symptomatic bone metastases. Several randomized control trials and meta-analyses have concluded a similar efficacy in pain relief when comparing single versus multiple fraction regimes. However, there continues to be reluctance to conform to published guidelines that recommend a single treatment for the palliation of painful bone metastases. The purpose of this literature review is to summarize international patterns of practice, and to determine if guidelines recommending single fraction treatment have been implemented in clinical care. Methods: A literature search was conducted in Ovid Medline, Embase, and Cochrane Central. Search words included, ‘bone metastases’, ‘radiation therapy’, ‘radiotherapy’, ‘patterns of practice’, and ‘dose fractionation’. Both prospective and retrospective studies that investigated the prescription of radiotherapy to bone metastases using actual patient databases were included. Articles were excluded if they investigated hypothetical scenarios. Results: Six hundred and thirteen results were generated from the literature search. Twenty-six articles met the inclusion criteria. Of these, 11 were Canadian, 8 were European, 6 were American, and 1 was Australian. The use of single fraction radiotherapy (SFRT) ranged from 3% to 75%, but was generally lower in American studies. Choice of fractionation depended on a variety of factors, including patient age, prognosis, site of irradiation, and physician experience. Conclusion: Despite the publication of robust randomized control trials, meta-analyses, and clinical practice guidelines recommending the use of a single treatment to palliate uncomplicated bone metastasis, SFRT is internationally underutilized.
doi:10.1016/j.jbo.2014.10.003
PMCID: PMC4723651  PMID: 26909305
Bone metastases; Radiation; Pattern of practice; Dose fractionation
11.  A Bayesian Meta-Analysis of Multiple Treatment Comparisons of Systemic Regimens for Advanced Pancreatic Cancer 
PLoS ONE  2014;9(10):e108749.
Background
For advanced pancreatic cancer, many regimens have been compared with gemcitabine (G) as the standard arm in randomized controlled trials. Few regimens have been directly compared with each other in randomized controlled trials and the relative efficacy and safety among them remains unclear.
Methods
A systematic review was performed through MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, and ASCO meeting abstracts up to May 2013 to identify randomized controlled trials that included advanced pancreatic cancer comparing the following regimens: G, G+5-fluorouracil, G+ capecitabine, G+S1, G+ cisplatin, G+ oxaliplatin, G+ erlotinib, G+ nab-paclitaxel, and FOLFIRINOX. Overall survival and progression-free survival with 95% credible regions were extracted using the Parmar method. A Bayesian multiple treatment comparisons was performed to compare all regimens simultaneously.
Results
Twenty-two studies were identified and 16 were included in the meta-analysis. Median overall survival, progression free survival, and response rates for G arms from all trials were similar, suggesting no significant clinical heterogeneity. For overall survival, the mixed treatment comparisons found that the probability that FOLFIRINOX was the best regimen was 83%, while it was 11% for G+ nab-paclitaxel and 3% for G+ S1 and G+ erlotinib, respectively. The overall survival hazard ratio for FOLFIRINOX versus G+ nab-paclitaxel was 0.79 [0.50–1.24], with no obvious difference in toxicities. The hazard ratios from direct pairwise comparisons were consistent with the mixed treatment comparisons results.
Conclusions
FOLFIRINOX appeared to be the best regimen for advanced pancreatic cancer probabilistically, with a trend towards improvement in survival when compared with other regimens by indirect comparisons.
doi:10.1371/journal.pone.0108749
PMCID: PMC4186762  PMID: 25286060
12.  Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries 
Nature protocols  2014;9(4):842-850.
Identifying the species on which hematophagous arthropods feed is crucial for studying the factors that affect pathogen distributions and that can aid public health. Here we describe a protocol to identify the species a parasitic arthropod has previously fed upon by identifying the source of the remnants of a previous blood meal via shotgun proteomics and spectral matching. The protocol is a nontargeted approach that uses the entire detected blood proteome for source identification; it does not require a priori knowledge of genome or protein sequences. Instead, reference spectral libraries are compiled from the blood of multiple host species by using SpectraST, which takes ~4 d; the identification of the species from which a previous blood meal of a hematophagous arthropod was taken is achieved with spectral matching against the reference spectral libraries, which takes approximately another 4 d. This method is robust against random degradation of the blood meal and can identify unknown blood remnants months after the feeding event.
doi:10.1038/nprot.2014.048
PMCID: PMC4179104  PMID: 24625782
13.  A repository of assays to quantify 10,000 human proteins by SWATH-MS 
Scientific Data  2014;1:140031.
Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).
doi:10.1038/sdata.2014.31
PMCID: PMC4322573  PMID: 25977788
14.  Quality Control of Danggui Buxue Tang, a Traditional Chinese Medicine Decoction, by 1H-NMR Metabolic Profiling 
Danggui Buxue Tang (DBT) is one of the simplest traditional Chinese medicine (TCM) decoctions, first described in China in 1247 AD. DBT is composed of 2 herbs, Astragali Radix (AR) and Angelica Sinensis Radix (ASR), boiled together in a 5 : 1 ratio. Clinically, DBT is prescribed to women as a remedy for menopausal symptoms. Here, H-NMR metabolic profiling was conducted for DBT and the water extracts of AR or ASR, to evaluate the potential of this chemical profiling method for quality control of the herbal decoction. Principal component analysis (PCA) showed that DBT could be readily distinguished from the water extracts of its constituent herbs by the metabolic profiles. More interestingly, the metabolic profile of DBT was not a simple sum of that of AR and ASR. Asparagine was found at significantly higher concentration in DBT than that in either AR or ASR extract, contributing mainly to the discrimination of DBT sample. In addition, we employed the same method to profile a commercial DBT powder, verifying its authenticity as compared to our prepared DBT. This study is the first to employ H-NMR metabolic profiling for the quality control of traditional Chinese medicine decoctions.
doi:10.1155/2014/567893
PMCID: PMC3980871  PMID: 24826194
15.  A complete mass spectrometric map for the analysis of the yeast proteome and its application to quantitative trait analysis 
Nature  2013;494(7436):266-270.
Complete reference maps or datasets, like the genomic map of an organism, are highly beneficial tools for biological and biomedical research. Attempts to generate such reference datasets for a proteome so far failed to reach complete proteome coverage, with saturation apparent at approximately two thirds of the proteomes tested, even for the most thoroughly characterized proteomes. Here, we used a strategy based on high-throughput peptide synthesis and mass spectrometry to generate a close to complete reference map (97% of the genome-predicted proteins) of the S. cerevisiae proteome. We generated two versions of this mass spectrometric map one supporting discovery- (shotgun) and the other hypothesis-driven (targeted) proteomic measurements. The two versions of the map, therefore, constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. The reference libraries can be browsed via a web-based repository and associated navigation tools. To demonstrate the utility of the reference libraries we applied them to a protein quantitative trait locus (pQTL) analysis, which requires measurement of the same peptides over a large number of samples with high precision. Protein measurements over a set of 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, impacting on the levels of related proteins. Our results suggest that selective pressure favors the acquisition of sets of polymorphisms that maintain the stoichiometry of protein complexes and pathways.
doi:10.1038/nature11835
PMCID: PMC3951219  PMID: 23334424
S. cerevisiae; selected reaction monitoring; SRM; MRM; spectral library; peptide library; mass spectrometric map; protein QTL
16.  Identifying sources of tick blood meals using unidentified tandem mass spectral libraries 
Nature communications  2013;4:1746.
Rapid and reliable identification of the vertebrate species on which a disease vector previously parasitized is imperative to study ecological factors that affect pathogen distribution and can aid the development of public health programs. Here we describe a proteome profiling technique designed to identify the source of blood meals of hematophagous arthropods. This method employs direct spectral matching and thus does not require a priori knowledge of any genetic or protein sequence information. Using this technology, we detect remnants of blood in blacklegged ticks (Ixodes scapularis) and correctly determine the vertebrate species from which the blood was derived even six months after the tick had fed. This biological fingerprinting methodology is sensitive, fast, cost-effective, and can potentially be adapted for other biological and medical applications when existing genome-based methods are impractical or ineffective.
doi:10.1038/ncomms2730
PMCID: PMC3635114  PMID: 23612287
17.  Chemical changes of Angelicae Sinensis Radix and Chuanxiong Rhizoma by wine treatment: chemical profiling and marker selection by gas chromatography coupled with triple quadrupole mass spectrometry 
Chinese Medicine  2013;8:12.
Background
Angelicae Sinensis Radix (ASR) and Chuanxiong Rhizoma (CR) can be treated with wine to promote their biological functions in Chinese medicine. Both ASR and CR contain similar volatile chemicals that could be altered after wine treatment. This study aims to identify the differential chemical profiles and to select marker chemicals of ASR and CR before and after wine treatment.
Methods
Chemical analyses were carried out by gas chromatography-triple quadrupole mass spectrometry (GC-QQQ-MS/MS) coupled with multivariate statistical analysis. Characterization of the compositions of essential oils was performed by automated matching to the MS library and comparisons of their mass spectra (NIST08 database). For ferulic acid, butylphthalide, Z-butylidenephthalide, senkyunolide A and Z-ligustilide, the mass spectrometer was operated in electron ionization mode, the selection reaction monitoring mode was used and an evaluation of the stability and sensitivity of the chromatographic system was performed for the tested extraction.
Results
Principal component analysis (PCA) simultaneously distinguished ASR and CR from different forms. Ferulic acid, Z-butylidenephthalide, Z-ligustilide, butylphthalide and senkyunolide A were screened by PCA loading plots and can be used as chemical markers for discrimination among different groups of samples.
Conclusion
Different chemical profiles of ASR and CR after wine treatment could be identified by GC-QQQ-MS/MS. The five marker chemicals selected by PCA, namely ferulic acid, butylphthalide, Z-butylidenephthalide, senkyunolide A and Z-ligustilide, were sufficient to distinguish between the crude and corresponding wine-treated forms of ASR and CR.
doi:10.1186/1749-8546-8-12
PMCID: PMC3693868  PMID: 23738580
18.  Statistical Platform to Discern Spatial and Temporal Coordination of Endothelial Sprouting 
Many biological processes, including angiogenesis, involve intercellular feedback and temporal coordination, but inference of these relations is often drowned in low sample sizes or noisy population data. To address this issue, a methodology was developed to statistically study spatial lateral inhibition and temporal synchronization in one specific biological process, endothelial sprouting mediated by Notch signaling. Notch plays an essential role in the development of organized vasculature, but the effects of Notch on the temporal characteristics of angiogenesis are not well understood. Results from this study showed that Notch lateral inhibition operates at distances less than 31μm. Furthermore, combining time lapse microscopy with an intraclass correlation model typically used to analyze family data showed intrinsic temporal synchronization among endothelial sprouts originating from the same microcarrier. Such synchronization was reduced with Notch inhibitors, but was enhanced with the addition of Notch ligands. These results indicate Notch plays a critical role in the temporal regulation of angiogenesis, as well as spatial control, and this method of analysis will be of significant utility in studies of a variety of other biological processes.
doi:10.1039/c2ib00057a
PMCID: PMC3654550  PMID: 22318325
19.  Skeletal morbidity rates over time in patients with bone metastases from solid tumors reported in bone modifying agents randomised trials 
Journal of Bone Oncology  2012;1(3):74-80.
Objective
Skeletal related events (SREs) are common in patients with bone metastases and lead to decreased quality of life and functional status. The definition of an SRE has evolved over the years and now excludes hypercalcemia of malignancy due to its low incidence. The purpose of this review was to investigate if advances in bone-targeted therapies have decreased skeletal morbidity rates (SMR) over time.
Methods
A literature search was conducted in several databases to identify phase III results from bone-targeted therapy trials from 1980 through September 2011. Graphs were created to document the trends of the natural log of SMR over the mean time of enrolment for all placebo and intervention arms. Statistical hypothesis testing was employed to account for confounding factors.
Results
A total of 14 studies were identified which reported the SMR from phase III trials from 1990 to 2007. A statistically significant downward trend was observed in the placebo arms of trials over time; a similar trend was seen in all intervention arms. In a direct comparison of intervention against placebo arms, it was found that there was a significant decreasing time trend (p<0.0001) and a significant departure in SMR from placebo to intervention arms (p=0.0348). These results were seen even after accounting for the confounding factors of histology and differences in drugs.
Conclusion
The decrease in SMR over time may not only be a result of advancements with bone targeted agents, but also due to better management and awareness of events associated with bone metastases.
doi:10.1016/j.jbo.2012.10.001
PMCID: PMC4723343  PMID: 26909260
Bisphosphonates; Bone metastases; Skeletal related events; Skeletal morbidity rates time trend
20.  Metabonomic analysis of water extracts from Chinese and American ginsengs by 1H nuclear magnetic resonance: identification of chemical profile for quality control 
Chinese Medicine  2012;7:25.
Background
With the gaining popularity of commercially prepared decoctions of herbal medicines on the market, an objective and efficient way to reveal the authenticity of such products is urgently needed. Previous attempts to use chromatographic or spectroscopic methods to identify ginseng samples made use of components derived from methanol extracts of the herb. It was not established that these herbs can be distinguished solely from consumable components, which are responsible for the clinical efficacy of the herb.
In this study, metabonomics, or metabolic profiling, based on the application of 1H-Nuclear Magnetic Resonance (NMR), is applied to distinguish the water extracts of three closely related ginseng species: P. ginseng (from two different cultivated regions in China), P. notoginseng and P. quinquefolius.
Methods
A water extraction protocol that mimics how ginseng decoctions are made for consumption was used to prepare triplicate samples from each herb for analysis. High-resolution 1H NMR spectroscopy was used to acquire metabolic profiles of the four ginseng samples. The spectral data were subjected to multivariate and univariate analysis to identify metabolites that were able to distinguish different types of ginseng.
Results
H NMR metabolic profiling was performed to distinguish the water extracts of P. ginseng cultivated in Hebei and Jilin of China, both of which were distinguished from extracts of P. notoginseng and P. quinquefolius, by unsupervised principle component analysis based on the entire 1H NMR spectral fingerprint Statistically significant differences were found for several discriminating features traced to common metabolites and the ginsenosides Rg1 and Rd, in the 1H NMR spectra.
Conclusion
This study demonstrated that 1H NMR metabonomics can simultaneously distinguish different ginseng species and multiple samples of the same species that were cultivated in different regions. This technique is applicable to the authentication and quality control of ginseng products.
doi:10.1186/1749-8546-7-25
PMCID: PMC3507782  PMID: 23140520
21.  Fast parallel tandem mass spectral library searching using GPU hardware acceleration 
Journal of proteome research  2011;10(6):2882-2888.
Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching) is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.
doi:10.1021/pr200074h
PMCID: PMC3107871  PMID: 21545112
CUDA; tandem mass spectrometry; spectral library searching; peptide identification
22.  Absolute quantification of microbial proteomes at different states by directed mass spectrometry 
The developed, directed mass spectrometry workflow allows to generate consistent and system-wide quantitative maps of microbial proteomes in a single analysis. Application to the human pathogen L. interrogans revealed mechanistic proteome changes over time involved in pathogenic progression and antibiotic defense, and new insights about the regulation of absolute protein abundances within operons.
The developed, directed proteomic approach allowed consistent detection and absolute quantification of 1680 proteins of the human pathogen L. interrogans in a single LC–MS/MS experiment.The comparison of 25 extensive, consistent and quantitative proteome maps revealed new insights about the proteome changes involved in pathogenic progression and antibiotic defense of L. interrogans, and about the regulation of protein abundances within operons.The generated time-resolved data sets are compatible with pattern analysis algorithms developed for transcriptomics, including hierarchical clustering and functional enrichment analysis of the detected profile clusters.This is the first study that describes the absolute quantitative behavior of any proteome over multiple states and represents the most comprehensive proteome abundance pattern comparison for any organism to date.
Over the last decade, mass spectrometry (MS)-based proteomics has evolved as the method of choice for system-wide proteome studies and now allows for the characterization of several thousands of proteins in a single sample. Despite these great advances, redundant monitoring of protein levels over large sample numbers in a high-throughput manner remains a challenging task. New directed MS strategies have shown to overcome some of the current limitations, thereby enabling the acquisition of consistent and system-wide data sets of proteomes with low-to-moderate complexity at high throughput.
In this study, we applied this integrated, two-stage MS strategy to investigate global proteome changes in the human pathogen L. interrogans. In the initial discovery phase, 1680 proteins (out of around 3600 gene products) could be identified (Schmidt et al, 2008) and, by focusing precious MS-sequencing time on the most dominant, specific peptides per protein, all proteins could be accurately and consistently monitored over 25 different samples within a few days of instrument time in the following scoring phase (Figure 1). Additionally, the co-analysis of heavy reference peptides enabled us to obtain absolute protein concentration estimates for all identified proteins in each perturbation (Malmström et al, 2009). The detected proteins did not show any biases against functional groups or protein classes, including membrane proteins, and span an abundance range of more than three orders of magnitude, a range that is expected to cover most of the L. interrogans proteome (Malmström et al, 2009).
To elucidate mechanistic proteome changes over time involved in pathogenic progression and antibiotic defense of L. interrogans, we generated time-resolved proteome maps of cells perturbed with serum and three different antibiotics at sublethal concentrations that are currently used to treat Leptospirosis. This yielded an information-rich proteomic data set that describes, for the first time, the absolute quantitative behavior of any proteome over multiple states, and represents the most comprehensive proteome abundance pattern comparison for any organism to date. Using this unique property of the data set, we could quantify protein components of entire pathways across several time points and subject the data sets to cluster analysis, a tool that was previously limited to the transcript level due to incomplete sampling on protein level (Figure 4). Based on these analyses, we could demonstrate that Leptospira cells adjust the cellular abundance of a certain subset of proteins and pathways as a general response to stress while other parts of the proteome respond highly specific. The cells furthermore react to individual treatments by ‘fine tuning' the abundance of certain proteins and pathways in order to cope with the specific cause of stress. Intriguingly, the most specific and significant expression changes were observed for proteins involved in motility, tissue penetration and virulence after serum treatment where we tried to simulate the host environment. While many of the detected protein changes demonstrate good agreement with available transcriptomics data, most proteins showed a poor correlation. This includes potential virulence factors, like Loa22 or OmpL1, with confirmed expression in vivo that were significantly up-regulated on the protein level, but not on the mRNA level, strengthening the importance of proteomic studies. The high resolution and coverage of the proteome data set enabled us to further investigate protein abundance changes of co-regulated genes within operons. This suggests that although most proteins within an operon respond to regulation synchronously, bacterial cells seem to have subtle means to adjust the levels of individual proteins or protein groups outside of the general trend, a phenomena that was recently also observed on the transcript level of other bacteria (Güell et al, 2009).
The method can be implemented with standard high-resolution mass spectrometers and software tools that are readily available in the majority of proteomics laboratories. It is scalable to any proteome of low-to-medium complexity and can be extended to post-translational modifications or peptide-labeling strategies for quantification. We therefore expect the approach outlined here to become a cornerstone for microbial systems biology.
Over the past decade, liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) has evolved into the main proteome discovery technology. Up to several thousand proteins can now be reliably identified from a sample and the relative abundance of the identified proteins can be determined across samples. However, the remeasurement of substantially similar proteomes, for example those generated by perturbation experiments in systems biology, at high reproducibility and throughput remains challenging. Here, we apply a directed MS strategy to detect and quantify sets of pre-determined peptides in tryptic digests of cells of the human pathogen Leptospira interrogans at 25 different states. We show that in a single LC–MS/MS experiment around 5000 peptides, covering 1680 L. interrogans proteins, can be consistently detected and their absolute expression levels estimated, revealing new insights about the proteome changes involved in pathogenic progression and antibiotic defense of L. interrogans. This is the first study that describes the absolute quantitative behavior of any proteome over multiple states, and represents the most comprehensive proteome abundance pattern comparison for any organism to date.
doi:10.1038/msb.2011.37
PMCID: PMC3159967  PMID: 21772258
absolute quantification; directed mass spectrometry; Leptospira interrogans; microbiology; proteomics
23.  Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast 
Science signaling  2010;3(153):rs4.
The phosphorylation and dephosphorylation of proteins by kinases and phosphatases constitute an essential regulatory network in eukaryotic cells. This network supports the flow of information from sensors through signaling systems to effector molecules, and ultimately drives the phenotype and function of cells, tissues, and organisms. Dysregulation of this process has severe consequences and is one of the main factors in the emergence and progression of diseases, including cancer. Thus, major efforts have been invested in developing specific inhibitors that modulate the activity of individual kinases or phosphatases; however, it has been difficult to assess how such pharmacological interventions would affect the cellular signaling network as a whole. Here, we used label-free, quantitative phosphoproteomics in a systematically perturbed model organism (Saccharomyces cerevisiae) to determine the relationships between 97 kinases, 27 phosphatases, and more than 1000 phosphoproteins. We identified 8814 regulated phosphorylation events, describing the first system-wide protein phosphorylation network in vivo. Our results show that, at steady state, inactivation of most kinases and phosphatases affected large parts of the phosphorylation-modulated signal transduction machinery, and not only the immediate downstream targets. The observed cellular growth phenotype was often well maintained despite the perturbations, arguing for considerable robustness in the system. Our results serve to constrain future models of cellular signaling and reinforce the idea that simple linear representations of signaling pathways might be insufficient for drug development and for describing organismal homeostasis.
doi:10.1126/scisignal.2001182
PMCID: PMC3072779  PMID: 21177495
24.  Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation datasets 
Proteomics  2010;10(6):1190-1195.
Electron transfer dissociation (ETD) is an alternative fragmentation technique to collision induced dissociation (CID) that has recently become commercially available. ETD has several advantages over CID. It is less prone to fragmenting amino acid side chains, especially those that are modified, thus yielding fragment ion spectra with more uniform peak intensities. Further, precursor ions of longer peptides and higher charge states can be fragmented and identified. However, analysis of ETD spectra has a few important differences that require the optimization of the software packages used for the analysis of CID data, or the development of specialized tools. We have adapted the Trans-Proteomic Pipeline (TPP) to process ETD data. Specifically, we have added support for fragment ion spectra from high charge precursors, compatibility with charge-state estimation algorithms, provisions for the use of the Lys-C protease, capabilities for ETD spectrum library building, and updates to the data formats to differentiate CID and ETD spectra. We show the results of processing datasets from several different types of ETD instruments and demonstrate that application of the ETD-enhanced TPP can increase the number of spectrum identifications at a fixed false discovery rate by as much as 100% over native output from a single sequence search engine.
doi:10.1002/pmic.200900567
PMCID: PMC3018683  PMID: 20082347
shotgun proteomics; electron-transfer dissociation; bioinformatics
25.  A Guided Tour of the Trans-Proteomic Pipeline 
Proteomics  2010;10(6):1150-1159.
The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of tandem mass spectrometry datasets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample dataset, demonstrating that the set up and use of the tools is straightforward and well supported and does not require specialized informatics resources or knowledge.
doi:10.1002/pmic.200900375
PMCID: PMC3017125  PMID: 20101611

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