Phylogene Specialized Analyses Laboratory Mass Spectrometry

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Mass spectrometry

Welcome on Phylogene’s website on Mass Spectrometry.

The recent developments of this technology contribute to important advances in our identification and authentication capabilities.

Our services are dedicated to food, environment, biotech, pharmaceutical, cosmetics companies as well as public or university laboratories.

Our goal is to allow you with our analytical methods to produce and to convert complex data into high value results.

Enjoy your visit!

link to phylogene.com


Proteomics

Proteomics has recently known huge development, particularly due to Mass Spectrometry.

This complex technology is now available for example in the hospital-based analysis laboratories. With MALDI-TOF it is now possible to identify bacterial species in a few minutes starting from a single colony on a plate.áWith tandem Mass Spectrometry SRM (Selected Reaction Monitoring) mode, the protein quantification is strongly improved, thus allowing to treat complex samples without preliminary costly and time consuming protein extraction steps.

The untargeted identification (said shotgun proteomics) and relative quantification of proteins (said label-free) now achieves such performances which allow samples comparisons such as treated vs control or pathologic vs safe.

These new advances produce huge amounts of data and needs new bioinformatics tool in order to process efficiently these data such as our CORAVALID module

Something to assess...

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TARGETED VS UNTARGETED

Approaches on therapeutic drug or cosmetic active ingredient effects are highly dependent on available analytical techniques. For the last 40 years, they have been driven by targeted techniques such as ELISA or PCR: These follow with narrow specificity, a particular molecule that has been identified as "the" marker of the biological phenomenon we want to track. So we study positive effects on a biological phenomenon, and then we look at the negative effects.

Recently, high-throughput sequencing techniques or LC-MS/MS introduced a drastic change in our way to assess an active molecule effects, as they allow identification and quantification of up to thousands of molecules at a time, without targeting beforehand. Such techniques generate masses of data, usually difficult to be processed which led us to rapidly develop complementary methods of Biostatistics and Bioinformatics as our CORAVALID method.

Also, given the results, usual reactions are along the line of "Where is my marker?". "Why all the molecules are moving?". "It's much more complicated than what I thought, so I will look at these first ..".

We do not have to be afraid of these innovative approaches. For instance, it is particularly fruitfulá understanding the molecular effects on a cell proteome by comparison of proteome of test vs. control. We quickly see the positive or negative impacts on metabolic pathways, biological and molecular functions, cell components and interactors.áHaving such information on early research stages is much more interesting as discovering it during later development. It avoids discovering it at a later development stage and of course at a higher cost !

In the lab these last few weeks

by nanoLC Dionex U3000 Q Exactive+ááá -áá Orbitrap:

Label-free quantitative comparison of S. cerevisiae proteomes...... Quantitative comparison of with metastatic evolution vs no evolution..... MRM method of pathogenic bacteria OMPs..... Shotgun identification of vegetal membrane structural protein..... Quantitative comparison of substratum corneum extracts, treated vs untreated.... Target study by ABPP (Activity Based Protein Profiling)..... Comparative study of HSV1 infected cells vs non-infected..... Label-free quantitative comparison of activated vs unactivated dendritic cells....

News

This site is a PHYLOGENE website

HolXplore: A new data processing module for host+microbiota outputs of omics comparison studies.

Probiotics: Multi-omics for probiotics studies and metaproteomics for mechanisms of action understanding.

Functional metabolism of microbiotas revealed by metaproteomics

XXIXth JED 2019 in Lyon Jan 31 - Feb 1st Presentation of our substantiation tools

Cancer: Proteomics in early-phase drug development and clinical trials for new biomarkers

Our posters at IFSCC2018: "Hypothesis free" proteomics and its dedicated bioinformatics efficient for studying the corneome and ceramidome of photodamaged SC, the secretome of fibroblasts, and effects of Prunus enzymatic extracts on skin explants.

Plant metaproteomics: Functional stability while taxonomic strong variability on phyllosphere.

Toxicity: Untargeted proteomics allows discovering positive effects and negative effects as well.

Publication: Prediction of the effects of an ingredient using our proteomics and bioinformatics approach.

RedOxMics: Evaluation of the abiotic stress of the skin and oxidation deepness.

CRISPR-Cas9 modifications checking: LC-MS/MS proteomics is a good tool for specific and unspecific modifications as well.

Functional microbiome: How to understand the interactions between host and microbiota through functions .

Our poster at ESDR2017: The possibilities of proteomics to study skin and its microbiome simultaneously at the functional level.

Post translational modifications: PTMs, an essential mechanism of protein functionality

Publication: Photodamage on stratum corneum investigated with proteomics

Phylogene and Dermatec collaboration on skin microbiome:
Based on its well established cohorts of volunteers and its qualified teams, Dermatec designs and realizes clinical trials in dermo-cosmetics with necessary specific biological samples dedicated to skin microbiome study.
On these samples, Phylogene does genomics and/or proteomics testing and associated bioinformatics /biostatistics data processing which highlight the effects on skin and its microbiome.
A good solution for your microbiome studies!

Probiotics: Proteomics and bioinformatics to understand the interactions between Lactobacilli and their environment.

AIS 2017: ADCs event: our poster

Microbiome: Example with our tools of proteomics able to track simultaneously effects on host and microbiome

Substantiation: An efficient innovative method

Fermentation: Understanding the yeast or bacteria fermentation process with LC-MS/MS proteomics

Understanding antimicrobial peptides mode of action: The ectodermal dysplasia skin secretome comparison vs controls by nanoLC-MS/MS proteomics gives a more complete understanding of the pathology

New nanoLC-MS/MS: MS Phylogene received this end of 2016 a nanoLC U3000 Dionex coupled to a Q-Exactive PLUS HCD Thermo for the best performances in proteomics and metabolomics.

IFSCC 2016: Our poster on MS proteomics of dryá skin in different ethnic groups has been awarded as one of the top 10 out of 313. It shows the power of the method in revealing new involved pathways.

Cosmetic 360 in Paris: A lot of interest of our combined genomic and proteomic approach of skin and microbiome.

Therapeutic antibodies: Host Cell Proteins (HCP) characterization by nanoLC-MS/MS

Nutrition: Studying the effects of a diet on muscle metabolism

Plant metabolism: Proteomics and phosphoproteomics to study the effects of environment.

Interactions between microbiome and host: metaproteomics is the tool able to see both simultaneously

Synergy meeting in Modena on Drug Development for Neglected Parasitic Diseases FP7 funded projects where Kindred project is one of the 4 projects: Our poster on kinases and kinases inhibition profiling.

SID 2016 (Society for Investigative Dermatology): Our poster on the UVs effects on stratum corneum determined by highres quantitative LC-MS/MS proteomics

FFPE and CANCER: NanoLC-MS/MS proteomics uses small parts of available slices to produce biomarkers or find targets

COSMETOLOGY: Oxidations follow-up by UVs

PLANT IMPROVEMENT: Proteomics and metabolomics are now mature

SKIN MICROBIOME: Metagenomics and proteomics to characterize products effects

JOURNEES JP MARTY: PEAU ET MICRORGANISMES 8-9 Dec 2015. This nice meeting updated us on skin microbiome

BIOMARKER AND DISCOVERY WORKFLOW: our poster at EBF 2015

RESISTANCE TO ANTIBIOTICS: Impact of rapid diagnostics on antibiotic misuse.

METAPROTEOMICS OF OUR MICROBIOME: The evolution of LC-MS/MS allows theá investigation of proteins in our saliva or skin or gut microbiome

STRESS RESISTANCE AND CROP PRODUCTIVITY: A review on advances in plant proteomics. Many LC-MS//MS proteomics tools are now efficient, also available at MS-PHYLOGENE

RESISTANCE TO ANTIBIOTICS:áááááá MS-PHYLOGENE is now using its PROTABIORES database to characterize antibiotic resistance mechanisms. This LC-MS/MS peptide and protein database contains 53000 entries in September 2015

DERMATOLOGY AND BIOMARKERS: A study starting with untargetd relative quantification of psoriatic skins proteins to get a first set of 47 moving proteins followed by MRM targeted method of these proteins. Then 8 proteins were selected for further validation. A kind of routine?

OPHTALMOLOGY: A study showed in 2011 the interest of tears to find biomarkers by LC/MS/MS for glaucoma; This new study shows that serum contains interesting proteins as biomarkers for uveitis which were found by label-free nanLC-MS/MS and which can be followed by MRM methods

CANCER: A study of phosphoproteins and signaling networks in bioological cell lines and tissues allows understanding induced effects by cancer and also drug resistance

COSMETOLOGY : A new study in mice on UVB effects on mouse skin. Our experience is different on human skin therefore it remains important to stay in untargeted mode to be sure to keep the whole effects on pathways rather than defining variable biomarkers.

LC-MS/MS MRM METHOD or ELISA? Do you know a multiplex LC-MS/MS MRM method can interestingly replace 20 ELISA methods at the development cost of 1 ELISA method?

Phylogene will be at Bio-Spring Europe in Paris , March 19-21, 2015

COSMETOLOGY: Substantiation tests byá comparison of proteome of fibroblasts, keratinocytes, skin explants, rebuilt skin, D-squame, skin swabs, extra-cellular matrix.. Please contact us for these services.

COSMETOLOGY NEWS: UV effects, skin disorders through fibroblasts proteomes, skin microbiome by Highres proteomics.

WOUND HEALING AND TISSUE REGENERATION: Proteins of interest by label-free LC-MS/MS

CANCEROLOGY: An example of biopsy comparison.

CANCEROLOGY: Kinome and kinases inhibitors by LC-MS/MS. Please contact us for these evaluations.

INFECTIOUS DISEASES: The infectious process of Dengue virus followed by HighRes proteomics. Please contact us for these tests.

VACCINES: The Outer Membrane Vesicles as a source of vaccine antigens.

STEM CELLS: Mechanisms and biomarkers of differentiation by HR proteomics.

DIABETES: Understanding the diabetic nephropathy by label-free LC-MS/MS.

SUNFLOWER: Leaf heterosis in label-free proteomics.

NEUROLOGICAL DISEASES: LC-MS/MS proteomics approach of Alzheimer disesase.

PROBIOTICS: The comparison of Bifidobacterium strains by label-free LC-MS/MS allows their differentiation in the process.

DuringáCosmetic days 2014 meeting, PHYLOGENE presented a poster: "High-resolution nano LC-MS/MS proteomics and CORAVALID data processing: For a new approach of substantiation tests "

Bioinformatics:CORAVALID

LC-MS/MS output data are rich but often large and complex to be treated. So it takes a lot of time to our customers.

CORAVALID performs a complementary analysis of identification and quantification data through a series of statistics tests. It allows exploiting all the wealth of your LC-MS/MS data.

PHYLOGENE-mass spectrometry has been granted by EUROSTARS for its NOSO-FIGHT project about Healthcare-Associated Infections.

PHYLOGENE-mass spectrometry is involved to the ID-THON project about tuna species identification

PHYLOGENE-mass spectrometry is partner of KINDReD, a FP7-Health-2013 Innovation project. The project is a 36 months and 14 partners project. Project aim is to develop drug candidate against kinetoplastids. PHYLOGENE- mass spectrometry is WP leader for drug's target determination.

PHYLOGENE will attend EIC 2013 onáSeptember 25th and 26th in Montpellier