Alexandre Panchaud

Aarhus University, Aarhus, Central Jutland, Denmark

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Publications (26)101.66 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Food peptidomics deals in part with the identification and quantification of nutritionally relevant peptides which are called bioactive peptides. This category of peptides comprises large, medium to small peptides. However, small peptides (2-6 amino acids) represent by far the largest category. Such molecules sit at the interface of both the world of proteomics and small molecule. The purpose of this study was to evaluate the feasibility of developing an LC-MSMS based method to measure such small peptides at a large scale that is representative of the hundreds of known small bioactive peptides. In order to do that we selected a very complex and homogeneous peptide set in terms of chemical and physical properties. This peptide set comprised only di, tri- and tetrapeptides made out the three branched chain amino acids (valine, leucine and isoleucine). Results showed that at least 60 % of these 117 peptides can be uniquely identified although many are isobaric and co-eluting. Moreover, identical results were obtained when spiked into a complex matrix, i.e. hydrolyzed whey protein. In conclusion, these results support the feasibility of a large scale approach and open the door to further development for all potential small bioactive peptides known so far.
    Journal of proteomics 03/2013; · 5.07 Impact Factor
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    ABSTRACT: Irritable bowel syndrome (IBS) is a functional gastrointestinal (GI) disorder characterized by chronic abdominal pain associated with alterations in bowel function. Given the heterogeneity of the symptoms, multiple pathophysiologic factors are suspected to play a role. We classified women with IBS into four subgroups based on distinct symptom profiles. In-depth shotgun proteomic analysis was carried out to profile the urinary proteomes to identify possible proteins associated with these subgroups. First void urine samples with urine creatinine level ≥100 mg/dL were used after excluding samples that tested positive for blood. Urine from 10 subjects representing each symptom subgroup was pooled for proteomic analysis. The urine proteome was analyzed by liquid chromatography–tandem mass spectrometry (LC–MS/MS) using a data-independent method known as Precursor Acquisition Independent From Ion Count (PAcIFIC) that allowed extended detectable dynamic range. Differences in protein quantities were determined by peptide spectral counting followed by validation of select proteins with ELISA or a targeted single reaction monitoring (LC–SRM/MS) approach. Four IBS symptom subgroups were selected: (1) Constipation, (2) Diarrhea + Low Pain, (3) Diarrhea + High Pain, and (4) High Pain + High Pychological Distress. A fifth group consisted of Healthy Control subjects. From comparisons of quantitative spectral counting data among the symptom subgroups and controls, a total of 18 proteins that showed quantitative differences in relative abundance and possible physiological relevance to IBS were selected for further investigation. Three of the 18 proteins were chosen for validation by either ELISA or SRM. An elevated expression of gelsolin (GSN) was associated with the high pain groups. Trefoil Factor 3 (TFF3) levels were higher in IBS groups compared to controls. In this study, the IBS patients subclassified by predominant symptoms showed differences in urine proteome levels. Proteins showing distinctive changes are involved in homeostasis of intestinal function and inflammatory response. These findings warrant future studies with larger, independent cohorts to enable more extensive assessment and validation of urinary protein markers as a diagnostic tool in adults with IBS.
    Journal of Proteome Research 10/2012; 11(12):5650–5662. · 5.06 Impact Factor
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    ABSTRACT: Staphylococcus aureus infections involve numerous adhesins and toxins, which expression depends on complex regulatory networks. Adhesins include a family of surface proteins covalently attached to the peptidoglycan via a conserved LPXTG motif. Here we determined the protein and mRNA expression of LPXTG proteins of S. aureus Newman in time course experiments, and their relation to fibrinogen adherence in vitro. Experiments were performed with mutants in the global accessory-gene regulator (agr), surface protein A (Spa) and fibrinogen-binding protein A (ClfA), as well as during growth in iron-rich or iron-poor media. Surface proteins were recovered by trypsin-shaving of live bacteria. Released peptides were analyzed by Liquid Chromatography coupled to Tandem Mass Spectrometry (LC-MS/MS). To unambiguously identify peptides unique to LPXTG-proteins, the analytical conditions were refined using a reference library of S. aureus LPXTG proteins heterogeneously expressed in surrogate Lactococcus lactis. Transcriptomes were determined by microarrays. Sixteen of the 18 LPXTG proteins present in S. aureus Newman were detected by proteomics. Nine LPXTG proteins showed a bell shape agr like expression that was abrogated in agr-negative mutants, including Spa, fibronectin-binding protein A (FnBPA), ClfA, iron-binding IsdA and IsdB, immunomodulator SasH, functionally uncharacterized SasD, biofilm-related SasG and methicillin resistance-related FmtB. However, only Spa and SasH modified their proteomic and mRNA profiles in parallel in the parent and its agr negative mutant, while all other LPXTG proteins modified their proteomic profiles independently of their mRNA. Moreover, ClfA became highly transcribed and active in fibrinogen adherence tests during late growth (24h), whereas it remained poorly detected by proteomics. On the other hand, iron-regulated IsdA-B-C increased their protein expression by >10 time in iron poor conditions. Thus, proteomic, transcriptomic and adherence phenotype demonstrated differential profiles in S. aureus. Moreover, trypsin peptide signatures suggested differential protein domain exposures in various environments, which might be relevant for anti-adhesin vaccines. A comprehensive understanding of the S. aureus physiology should integrate all three approaches.
    Molecular &amp Cellular Proteomics 07/2012; · 7.25 Impact Factor
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    Martin Kussmann, Michael Affolter, Alexandre Panchaud
    Journal of proteomics 03/2012; 75(12):3381-5. · 5.07 Impact Factor
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    Alexandre Panchaud, Michael Affolter, Martin Kussmann
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    ABSTRACT: We describe nutritional peptidomics for discovery and validation of bioactive food peptide and their health effects. Understanding nature and bioactivity of nutritional peptides means comprehending an important level of environmental regulation of the human genome, because diet is the environmental factor with the most profound life-long influence on health. We approach the theme from three angles, namely the analysis, the discovery and the biology perspective. Food peptides derive from parent food proteins via in vitro hydrolysis (processing) or in vivo digestion by various unspecific and specific proteases, as opposed to the tryptic peptides typically generated in biomarker proteomics. A food bioactive peptide may be rare or unique in terms of sequence and modification, and many food genomes are less well annotated than e.g. the human genome. Bioactive peptides can be discovered either empirically or by prediction: we explain both the classical hydrolysis strategy and the bioinformatics-driven reversed genome engineering. In order to exert bioactivity, food peptides must be either ingested and then reach the intestine in their intact form or be liberated in situ from their parent proteins to act locally, that is in the gut, or even systemically, i.e. through the blood stream. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
    Journal of proteomics 12/2011; 75(12):3546-59. · 5.07 Impact Factor
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    ABSTRACT: A label-free quantitative variation of the recently developed data-independent shotgun proteomic method precursor acquisition independent from ion count (PAcIFIC) was used to identify novel proteins implicated in cancer progression and resistance. Specifically, this screen identified the pro-metastatic protein anterior gradient 2 (AGR2) as significantly up-regulated in tamoxifen-treated cells. Highlighting the need for direct proteome profiling methods like PAcIFIC, neither data-dependent gas-phase fractionation nor a transcriptomic screen detected AGR2 protein/transcript at significantly up-regulated levels. Further cell-based experiments using human cancer cell lines and in vivo xenografts confirmed the PAcIFIC hypothesis that AGR2 is up-regulated in MCF-7 cells post tamoxifen treatment and that it is implicated in drug resistance mediation.
    Journal of Proteome Research 09/2011; 10(10):4567-78. · 5.06 Impact Factor
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    ABSTRACT: Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, this bottom-up method presents major drawbacks in terms of detectable dynamic range. Recently, we demonstrated the superior performance of a data-independent method we termed precursor acquisition independent from ion count (PAcIFIC). Here, we report a faster, accurate, multiplexed, and quantitative PAcIFIC method. Our results show that the time needed to perform such analysis can be decreased by 33% to 66% using modern ion trap instruments and that high mass accuracy can be applied to such a strategy. Quantification capability is demonstrated on protein standards and a whole bacterial cell lysate using isobaric tagging. Finally, we confirm in yeast the dynamic range capabilities of such a method where proteins down to less than 50 copies per cell can be monitored without sample prefractionation.
    Analytical Chemistry 02/2011; 83(6):2250-7. · 5.82 Impact Factor
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    ABSTRACT: Abdominal aortic aneurysm (AAA) is characterized by increased aortic vessel wall diameter (>1.5 times normal) and loss of parallelism. This disease is responsible for 1-4% mortality occurring on rupture in males older than 65 years. Due to its asymptomatic nature, proteomic techniques were used to search for diagnostic biomarkers that might allow surgical intervention under nonlife threatening conditions. Pooled human plasma samples of 17 AAA and 17 control patients were depleted of the most abundant proteins and compared using a data-independent shotgun proteomic strategy, Precursor Acquisition Independent From Ion Count (PAcIFIC), combined with spectral counting and isobaric tandem mass tags. Both quantitative methods collectively identified 80 proteins as statistically differentially abundant between AAA and control patients. Among differentially abundant proteins, a subgroup of 19 was selected according to Gene Ontology classification and implication in AAA for verification by Western blot (WB) in the same 34 individual plasma samples that comprised the pools. From the 19 proteins, 12 were detected by WB. Five of them were verified to be differentially up-regulated in individual plasma of AAA patients: adiponectin, extracellular superoxide dismutase, protein AMBP, kallistatin and carboxypeptidase B2. Plasma depletion of high abundance proteins combined with quantitative PAcIFIC analysis offered an efficient and sensitive tool for the screening of new potential biomarkers of AAA. However, WB analysis to verify the 19 PAcIFIC identified proteins of interest proved inconclusive save for five proteins. We discuss these five in terms of their potential relevance as biological markers for use in AAA screening of population at risk.
    PLoS ONE 01/2011; 6(12):e28698. · 3.53 Impact Factor
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    ABSTRACT: Postnatal intestinal development is a very dynamic process characterized by substantial morphological changes that coincide with functional adaption to the nutritional change from a diet rich in fat (milk) to a diet rich in carbohydrates on from weaning. Time-resolved studies of intestinal development have so far been limited to investigation at the transcription level or to single or few proteins at a time. In the present study, we elucidate proteomic changes of primary intestinal epithelial cells from jejunum during early suckling (1-7 days of age), middle suckling (7-14 days), and weaning period (14-35 days) in mice, using a label-free proteomics approach. We show differential expression of 520 proteins during intestinal development and a pronounced change of the proteome during the middle suckling period and weaning. Proteins involved in several metabolic processes were found differentially expressed along the development. The temporal expression profiles of enzymes of the glycolysis were found to correlate with the increase in carbohydrate uptake at weaning, whereas the abundance changes of proteins involved in fatty acid metabolism as well as lactose metabolism indicated a nondiet driven preparation for the nutritional change at weaning. Further, we report the developmental abundance changes of proteins playing a vital role in the neonatal acquisition of passive immunity. In addition, different isoforms of several proteins were quantified, which may contribute to a better understanding of the roles of the specific isoforms in the small intestine. In summary, we provide a first, time-resolved proteome profile of intestinal epithelial cells along postnatal intestinal development.
    Molecular &amp Cellular Proteomics 12/2010; 10(3):M110.005231. · 7.25 Impact Factor
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    Martin Kussmann, Alexandre Panchaud, Michael Affolter
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    ABSTRACT: Food and beverages are the only physical matter we take into our body, if we disregard the air we inhale and the drugs we may have to apply. While traditional nutrition research has aimed at providing nutrients to nourish populations and preventing specific nutrient deficiencies, it more recently explores health-related aspects of individual bioactive components as well as entire diets and this at group rather than population level. The new era of nutrition research translates empirical knowledge to evidence-based molecular science. Modern nutrition research focuses on promoting health, preventing or delaying the onset of disease, optimizing performance, and assessing risk. Personalized nutrition is a conceptual analogue to personalized medicine and means adapting food to individual needs. Nutrigenomics and nutrigenetics build the science foundation for understanding human variability in preferences, requirements, and responses to diet and may become the future tools for consumer assessment motivated by personalized nutritional counseling for health maintenance and disease prevention. The scope of this paper is to review the current and future aspects of nutritional proteomics, focusing on the two main outputs: identification of health biomarkers and analysis of food bioactives.
    Journal of Proteome Research 10/2010; 9(10):4876-87. · 5.06 Impact Factor
  • Pragya Singh, Alexandre Panchaud, David R Goodlett
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    ABSTRACT: Protein complexes are the foundation of a majority of cellular processes. Although a large number of protein complexes have been identified through biochemical experiments, the precise molecular details and three-dimensional structures are available for only a small fraction. Chemical cross-linking coupled with mass spectrometry (CXMS) has gained popularity in recent years for characterization of inter- and intraprotein interactions in protein complexes. This perspective provides a comprehensive and critical overview of CXMS strategies employed for structural elucidation of protein complexes. We evaluate the challenges associated with CXMS techniques with special emphasis on data analysis. As sensitivity, mass resolution, mass accuracy and ease of use of mass spectrometers have improved, the complexity of processing and interpreting CXMS data has become the central problem to be addressed. We review here a number of computer programs available to address these problems.
    Analytical Chemistry 03/2010; 82(7):2636-42. · 5.82 Impact Factor
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    ABSTRACT: We developed an informatic method to identify tandem mass spectra composed of chemically cross-linked peptides from those of linear peptides and to assign sequence to each of the two unique peptide sequences. For a given set of proteins the key software tool, xComb, combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files. The xComb library of select theoretical cross-linked peptides may then be used as a database that is examined by a standard proteomic search engine to match tandem mass spectral data sets to identify cross-linked peptides. The database search may be conducted against as many as 50 proteins with a number of common proteomic search engines, e.g. Phenyx, Sequest, OMSSA, Mascot and X!Tandem. By searching against a peptide library of linearized, cross-linked peptides, rather than a linearized protein library, search times are decreased and the process is decoupled from any specific search engine. A further benefit of decoupling from the search engine is that protein cross-linking studies may be conducted with readily available informatics tools for which scoring routines already exist within the proteomic community.
    Journal of Proteome Research 03/2010; 9(5):2508-15. · 5.06 Impact Factor
  • S. Chen, A. Panchaud, D. Goodlett, S. Shaffer
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    ABSTRACT: RP-101
    01/2010;
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    ABSTRACT: Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, this bottom-up method presents major drawbacks in terms of detectable dynamic range. Here, we demonstrate the superior performance of a data-independent method we term precursor acquisition independent from ion count (PAcIFIC). Our results show that almost the entire, predicted, soluble bacterial proteome can be thoroughly analyzed by PAcIFIC without the need for any sample fractionation other than the C18-based liquid chromatograph used to introduce the peptide mixture into the mass spectrometer. Importantly, we also show that PAcIFIC provides unique performance for analysis of human plasma in terms of the number of proteins identified (746 at FDR < or = 0.5%) and achieved dynamic range (8 orders of magnitude at FDR < or = 0.5%), without any fractionation other than immuno-depletion of the seven most abundant proteins.
    Analytical Chemistry 07/2009; 81(15):6481-8. · 5.82 Impact Factor
  • Alexandre Panchaud, Scott A. Shaffer, David R. Goodlett
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    ABSTRACT: The vast majority of shotgun proteomics experiments are conducted using data-dependent precursor ion selection; i.e. ions are selected for MS2 fragmentation based on: 1) presence of a signal, and 2) intensity. While very popular and successful, this approach suffers from limited dynamic range. Recently, we presented a data-independent acquisition method showing superior performance on serum analysis (eight orders of magnitude dynamic range) that we named Precursor Acquisition Independent From Ion Count (PAcIFIC). Here, we present a novel quantitative, multiplexed PAcIFIC workflow. Protein samples are labelled using isobaric tagging approaches, e.g. TMT (ThermoFisher). A collision induced dissociation (CID) spectrum is acquired every 1.5 m/z value whether a precursor ion is observed or not followed by a pulse-Q dissociation (PQD) spectrum in the low m/z range where TMT reporter ions are expected. Thus, in a single LC-MS/MS experiment 30 such scans are acquired (i.e. 15 pairs of CID/PQD) across a range of 22.5 m/z. Repeated injections are preformed in an identical fashion until the desired m/z mass range is achieved. CID and PQD spectra are merged into a single composite spectrum using in-house software, searched with Sequest, validated using FDR < 1% and quantified using Libra (TPP, ISB, Seattle).Two reference sets were designed with 14 protein standards. Theoretical ratios spanned from 0.1 to 10 (reporter 126 over 127). All 14 proteins were identified in average with >80% sequence coverage and the expected ratios for the 14 proteins matched to less than 20% deviation. A similar experiment was conducted on a whole cell lysate of Pseudomonas aeruginosa. Twice the same amount of digest was tagged to mimic a 1:1 ratio distribution. A total of 1400 proteins were identified at FDR<0.5% of which 800 were quantified. The average/median ratio distribution was 1.01/1.00 with a standard deviation of 0.15.
    64th American Chemical Society Northwestern General Meeting; 06/2009
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    ABSTRACT: The increasing number of completely sequenced bacterial genomes allows comparing their architecture and genetic makeup. Such new information highlights the crucial role of lateral genetic exchanges in bacterial evolution and speciation. Here we analyzed the twelve sequenced genomes of Streptococcus pyogenes by a naïve approach that examines the preferential nucleotide usage along the chromosome, namely the usage of G versus C (GC-skew) and T versus A (TA-skew). The cumulative GC-skew plot presented an inverted V-shape composed of two symmetrical linear segments, where the minimum and maximum corresponded to the origin and terminus of DNA replication. In contrast, the cumulative TA-skew presented a V-shape, which segments were interrupted by several steep slopes regions (SSRs), indicative of a different nucleotide composition bias. Each S. pyogenes genome contained up to nine individual SSRs, encompassing all described strain-specific prophages. In addition, each genome contained a similar unique non-phage SSR, the core of which consisted of 31 highly homologous genes. This core includes the M-protein, other mga-related factors and other virulence genes, totaling ten intrinsic virulence genes. In addition to a high content in virulence-related genes and to a peculiar nucleotide bias, this SSR, which is 47 kb-long in a M1GAS strain, harbors direct repeats and a tRNA gene, suggesting a mobile element. Moreover, its complete absence in a M-protein negative group A Streptococcus natural isolate demonstrates that it could be spontaneously lost, but in vitro deletion experiments indicates that its excision occurred at very low rate. The stability of this SSR, combined to its presence in all sequenced S. pyogenes sequenced genome, suggests that it results from an ancient acquisition. Thus, this non-phagic SSR is compatible with a pathogenicity island, acquired before S. pyogenes speciation. Its potential excision might bear relevance for vaccine development, because vaccines targeting M-protein might select for M-protein-negative variants that still carry other virulence determinants.
    BMC Genomics 05/2009; 10:198. · 4.40 Impact Factor
  • Archives of Cardiovascular Diseases - ARCH CARDIOVASC DIS. 01/2009; 102.
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    ABSTRACT: Staphylococcus aureus experimental endocarditis relies on sequential fibrinogen binding (for valve colonization) and fibronectin binding (for endothelial invasion) conferred by peptidoglycan-attached adhesins. Fibronectin-binding protein A (FnBPA) reconciles these two properties--as well as elastin binding--and promotes experimental endocarditis by itself. Here we attempted to delineate the minimal subdomain of FnBPA responsible for fibrinogen and fibronectin binding, cell invasion, and in vivo endocarditis. A large library of truncated constructs of FnBPA was expressed in Lactococcus lactis and tested in vitro and in animals. A 127-amino-acid subdomain spanning the hinge of the FnBPA fibrinogen-binding and fibronectin-binding regions appeared necessary and sufficient to confer the sum of these properties. Competition with synthetic peptides could not delineate specific fibrinogen- and fibronectin-binding sites, suggesting that dual binding arose from protein folding, irrespective of clearly defined binding domains. Moreover, coexpressing the 127-amino-acid subdomain with remote domains of FnBPA further increased fibrinogen binding by > or =10 times, confirming the importance of domain interactions for binding efficacy. In animals, fibrinogen binding (but not fibronectin binding) was significantly associated with endocarditis induction, whereas both fibrinogen binding and fibronectin binding were associated with disease severity. Moreover, fibrinogen binding also combined with fibronectin binding to synergize the invasion of cultured cell lines significantly, a feature correlating with endocarditis severity. Thus, while fibrinogen binding and fibronectin binding were believed to act sequentially in colonization and invasion, they appeared unexpectedly intertwined in terms of both functional anatomy and pathogenicity (in endocarditis). This unforeseen FnBPA subtlety might bear importance for the development of antiadhesin strategies.
    Infection and immunity 09/2008; 76(8):3824-31. · 4.21 Impact Factor
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    ABSTRACT: Identification and relative quantification of hundreds to thousands of proteins within complex biological samples have become realistic with the emergence of stable isotope labeling in combination with high throughput mass spectrometry. However, all current chemical approaches target a single amino acid functionality (most often lysine or cysteine) despite the fact that addressing two or more amino acid side chains would drastically increase quantifiable information as shown by in silico analysis in this study. Although the combination of existing approaches, e.g. ICAT with isotope-coded protein labeling, is analytically feasible, it implies high costs, and the combined application of two different chemistries (kits) may not be straightforward. Therefore, we describe here the development and validation of a new stable isotope-based quantitative proteomics approach, termed aniline benzoic acid labeling (ANIBAL), using a twin chemistry approach targeting two frequent amino acid functionalities, the carboxylic and amino groups. Two simple and inexpensive reagents, aniline and benzoic acid, in their (12)C and (13)C form with convenient mass peak spacing (6 Da) and without chromatographic discrimination or modification in fragmentation behavior, are used to modify carboxylic and amino groups at the protein level, resulting in an identical peptide bond-linked benzoyl modification for both reactions. The ANIBAL chemistry is simple and straightforward and is the first method that uses a (13)C-reagent for a general stable isotope labeling approach of carboxylic groups. In silico as well as in vitro analyses clearly revealed the increase in available quantifiable information using such a twin approach. ANIBAL was validated by means of model peptides and proteins with regard to the quality of the chemistry as well as the ionization behavior of the derivatized peptides. A milk fraction was used for dynamic range assessment of protein quantification, and a bacterial lysate was used for the evaluation of relative protein quantification in a complex sample in two different biological states.
    Molecular &amp Cellular Proteomics 05/2008; 7(4):800-12. · 7.25 Impact Factor
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    ABSTRACT: Proteomics has come a long way from the initial qualitative analysis of proteins present in a given sample at a given time ("cataloguing") to large-scale characterization of proteomes, their interactions and dynamic behavior. Originally enabled by breakthroughs in protein separation and visualization (by two-dimensional gels) and protein identification (by mass spectrometry), the discipline now encompasses a large body of protein and peptide separation, labeling, detection and sequencing tools supported by computational data processing. The decisive mass spectrometric developments and most recent instrumentation news are briefly mentioned accompanied by a short review of gel and chromatographic techniques for protein/peptide separation, depletion and enrichment. Special emphasis is placed on quantification techniques: gel-based, and label-free techniques are briefly discussed whereas stable-isotope coding and internal peptide standards are extensively reviewed. Another special chapter is dedicated to software and computing tools for proteomic data processing and validation. A short assessment of the status quo and recommendations for future developments round up this journey through quantitative proteomics.
    Journal of Proteomics 05/2008; 71(1):19-33. · 4.09 Impact Factor

Publication Stats

346 Citations
101.66 Total Impact Points

Institutions

  • 2012
    • Aarhus University
      Aarhus, Central Jutland, Denmark
  • 2009–2011
    • University of Washington Seattle
      • Department of Medicinal Chemistry
      Seattle, WA, United States
  • 2010
    • Nestlé S.A.
      Vevey, Vaud, Switzerland
    • University of Southern Denmark
      • Department of Biochemistry and Molecular Biology
      Copenhagen, Capital Region, Denmark
  • 2006–2009
    • University of Lausanne
      • • Department of Fundamental Microbiology (DMF)
      • • Faculté de biologie et de médecine (FBM)
      Lausanne, VD, Switzerland
  • 2008
    • Centre Hospitalier Universitaire de Dijon
      • Department of Infectious Diseases
      Dijon, Bourgogne, France