MartinProtean trusted for the toughest analyses, appreciated for the responsive customer service.

MartinProtean has a wealth of experience in identifying and quantifying covalent modifications to protein sequences.  We specialize in several challenging analyses: We identify the sites and quantify the extent of covalent modification of experimentally modified proteins by nanoLCMSn; we perform the protein processing and nanoLCMSn analysis for protein structure studies involving covalent modification including phi value analyses and we confirm the identity of the correct disulfides in biotherapeutic leads by nanoLCMSn.

Experimentally introduced covalently modified protein reagents are ubiquitous in life science research.  From flurophore-labeled secondary antibodies in two-photon microscopy to SHG sensitive probes in surface plasmon resonance detection of protein confirmation, these chemically modified reagent proteins enable research progress. But our incomplete understanding of the nature of those modifications limits that progress.  MartinProtean performs the experiments necessary to complete that understanding.

Experimentally introduced modifications are more challenging to characterize than biological post-translational modifications as the experimentally introduced modifications lack biological site specificity and the site occupancy may be lower than one percent, rather than close to complete.  Identifying probe labeled sites on reagent proteins as well as sites modified in phi value structure studies can be confounded if the protein processing necessary for the LCMSn experiment perturbs the often more labile label linkages prior to analysis. To complete quantification of the extent of modification at the modified sites for reagent proteins and in protein structure studies, it is highly desirable to attain a quantification of every peptide containing modifiable residues in the sequence from both modified and unmodified protein samples.  When identifying unexpected modified peptides from fragmentation mass spectra as well as assigning disulfide linked di- and tripeptides specialized software and experience manually analyzing spectra are central to successful comprehension of the data.

MartinProtean uses its own protein processing protocols (to our knowledge significantly different from those present in the published literature.) Our protocols achieve a more complete sequence coverage with a more uniform yield of peptide, addressing a known challenge in de novo antibody sequencing work.   Our protocols also avoid cleaving highly occupied but labile probe linkages that are cleaved with standard published methods and frequently present in the samples we see.  MartinProtean quantifies both the total amount of probe per protein as well as the amount of probe at each labeled site using an analytically rigorous and comprehensive accounting of the modifiable sites on the protein.  We have found our approach to be more reliable in obtaining a coherent description of the modified state of the protein and it is a considerable extension of what we were able to find in the published work.

Some of our valued clients:

                                        
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chemically modified protein analysis

Chemically modified proteins are ubiquitous reagents in life science discovery.  While these proteins are generally used without characterization this practice produces confounding factors that limit the probity of experimental results.  Whether your SPR data that does not produce a satisfying fit to the simple 1:1 stoichiometry that you think is correct or it is the punctate antibody fluorescence in the endoplasmic reticulum that you expected to see only on the golgi, uncharacterized chemically modified proteins can be largely responsible. Let Martin-Protean characterize these reagents, and improve your ability to perform and analyze experiments with them.

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protein structure phi value analysis

Probing protein structure by measuring differential intrinsic rates of reactivity to chemical probes at different amino acid residues is used to elucidate the folding pathways of proteins of interest.  The extensive expertise in understanding protein structure, the chemical modification of proteins, and LCMSMS  analysis of chemically modified proteins makes Martin-Protean the goto CRO for comprehensive, sensitive LCMSMS readout of all your phi value analysis experiments.

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biologic disulfide validation

Developing a unique biologic can involve extended periods of uncertainty regarding your molecular entity's conforming to design specifications. A powerful and robust method for insuring that your expression/post-translational modification/mutation change still produces the properly folded protein is to confirm that the protein still retains its native disulfides at native levels of occupancy. The Martin-Protein expertise in protein processing for LCMSMS, protein fragmentation and crosslinked peptide assignments has made us the leader in identifying even double disulfide tripeptides from LCMSMS fragmentation spectra.

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