Protein characterization: 

1. protein/peptide analysis by HPLC/MS and MS/MS;
2. sample purification (zip tip or similar) and intact protein MW determination by nanospray off line MS.

Protein identification: PMF and sequencing

1. PTM-characterization: validation by Western Blotting and 2DE +/- removal of the PTM (glycosylation, phosphorylation);
2. phosphorylation characterization by TiO2 or IMAC enrichment and mass spectrometry;
3. identification of a spot or band by in gel digestion and LC-MS/MS .

Quantitative protein profiling by mass spectrometry and statistical analysis. Differential protein display in two or more diverse conditions using:

1.  iTRAQ or TMT labelling of peptides,
2.  SILAC methodology,
3.  Label-free approach.

Biomarker profiling in biological samples by 2DE, image analysis and statistical evaluation. Differential protein display in two or more diverse conditions in plasma, serum, urine, tissue.

Metabolomics/Lipidomics by mass spectrometry and statistical analysis. Untargeted workflow for differential small molecules/lipids display in: plasma, serum, urine, tissues.

Quantitative Metabolomics/Lipidomics by mass spectrometry and statistical analysis. Targeted workflow for specific small molecules/lipids display in plasma, serum, urine, tissues.

ACTIVITIES	PROCESSING TIME
Protein characterization
Protein and peptide analysis by HPLC/MS and MS/MS	3 days
Sample purification (zip tip or similar) and intact protein MW determination by MALDI or nanospray off line MS	3 days
Protein identification: PMF and sequencing
PTM-characterization: validation by Western Blotting and 2DE +/- removal of the PTM (glycosylation, phosphorylation)	2 weeks
Phosphorylation characterization by TiO2 or IMAC enrichment and mass spectrometry	2 weeks
Identification of a spot or band by in gel digestion and LC-MS/MS	1 week

Processing timing depends on the number of samples for:

• Biomarker profiling in biological samples by 2DE, image analysis and statistical evaluation. Differential protein display in two or more diverse conditions in: plasma; serum; urine; tissues.
• Quantitative protein profiling by mass spectrometry and statistical analysis. Differential protein display in two or more diverse conditions using: iTRAQ or TMT labelling of peptide; SILAC methodology;Label-fre approach.
• Metabolomics/Lipidomics by mass spectrometry and statistical analysis. Untargeted workflow for differential small molecules/lipids display in: plasma; serum; urine; tissues.
• Quantitative Metabolomics/Lipidomics by mass spectrometry and statistical analysis. Targeted workflow for specific small molecules/lipids display in: plasma; serum; urine; tissues.

In case of maintenance or out of order instrumentation as well as when multiple samples are submitted, the processing time can be longer.

Output of the results will be sent in an Excel or Word format, along with information on: mass spectrometer settings, protein database version, search parameters, experimental conditions for 2DE, constraints for image analysis and statistical evaluation.
When the Facility will send the results of the analysis (by fax or e-mail) then the Grant Office will give the invoice to the user for the payment.

Ferrari A, Longo R, Fiorino E, Silva R, Mitro N, Cermenati G, Gilardi F, Desvergne B, Andolfo A, Magagnotti C, Caruso D, Fabiani E, Hiebert SW, Crestani M. HDAC3 is a molecular brake of the metabolic switch supporting white adipose tissue browning. Nat Commun. 2017 Jul 21;8(1):93. doi: 10.1038/s41467-017-00182-7.

Drago D, Basso V, Gaude E, Volpe G, Peruzzotti-Jametti L, Bachi A, Musco G, Andolfo A, Frezza C, Mondino A, Pluchino S. Metabolic determinants of the immune modulatory function of neural stem cells. J Neuroinflammation. 2016 Sep 2;13(1):232. doi: 10.1186/s12974-016-0667-7.

Nebuloni M, Albarello L, Andolfo A, Magagnotti C, Genovese L, Locatelli I, Tonon G, Longhi E, Zerbi P, Allevi R, Podestà A, Puricelli L, Milani P, Soldarini A, Salonia A, Alfano M. Insight on colorectal carcinoma infiltration by studying perilesional extracellular matrix.  Sci Rep. 2016 Mar 4; 6:22522. doi: 10.1038/srep22522.

Brunati M, Perucca S, Han L, Cattaneo A, Consolato F, Andolfo A, Schaeffer C, Olinger E, Peng J, Santambrogio S, Perrier R, Li S, Bokhove M, Bachi A, Hummler E, Devuyst O, Wu Q, Jovine L, Rampoldi L. The serine protease hepsin mediates urinary secretion and polymerisation of Zona Pellucida domain protein uromodulin. Elife. 2015 Dec 17;4. pii: e08887. doi: 10.7554/eLife.08887.

Barbariga M, Curnis F, Andolfo A, Zanardi A, Lazzaro M, Conti A, Magnani G, Volontè MA, Ferrari L, Comi G, Corti A, Alessio M. Ceruloplasmin functional changes in Parkinson’s disease-cerebrospinal fluid. Mol Neurodegener. 2015 Nov 4; 10: 59. doi: 10.1186/s13024-015-0055-2.

D’Addio F, La Rosa S, Maestroni A, Jung P, Orsenigo E, Ben Nasr M, Tezza S, Bassi R, Finzi G, Marando A, Vergani A, Frego R, Albarello L, Andolfo A, Manuguerra R, Viale E, Staudacher C, Corradi D, Batlle E, Breault D, Secchi A, Folli F, Fiorina P. Circulating IGF-I and IGFBP3 levels control human colonic stem cell function and are disrupted in diabetic enteropathy. Cell Stem Cell. 2015 Oct 1;17(4):486-98. doi: 10.1016/j.stem.2015.07.010.

Barbariga M, Curnis F, Spitaleri A, Andolfo A, Zucchelli C, Lazzaro M, Magnani G, Musco G, Corti A, Alessio M. Oxidation-induced structural changes of ceruloplasmin foster NGR motif deamidation that promotes integrin binding and signaling. Biol. Chem. 2014 Feb 7; 289(6):3736-48. doi: 10.1074/jbc.M113.520981. Epub 2013 Dec 23.

Magagnotti C, Matassa PG, Bachi A, Vendettuoli V, Fermo I, Colnaghi MR, Carletti RM, Mercadante D, Fattore E, Mosca F, Andolfo A. Calcium signaling-related proteins are associated with broncho-pulmonary dysplasia progression. Proteomics. 2013 Dec 6; 94: 401-12. doi: 10.1016/j.jprot.2013.10.007. Epub 2013 Oct 16.