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| Investigators | Sample type | Proteomics techniques | Outcome |
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Immuno affinity MS Advantages: Identify mutations on known amyloid proteins. Disadvantages: Only applicable to known amyloid proteins; Require antibody of high specificity; Mutation may destroy antigenic epitope, leading to reduction of antibody binding; Amyloid proteins may deposit in tissues leading to low serum levels; Not as efficient as DNA sequencing. | Tachibana et al. [29] | Serum | Immunoprecipitation, MALDI-TOF | Spectral pattern matching to genetic mutation |
Sen et al. [44] | Serum, cerebrospinal fluid | On-line immunoaffinity capture, ESI-MS | Informations on relative abundance of protein isoforms, requires specific antibodies |
Bergen et al. [28, 45] | Serum | Automated-online affinity purification, ESI-MS | Clinical assay to detect transthyretin mutations |
Nepomuceno et al. [46] | Serum | Immunoprecipitation, Fourier-transform ion-cyclotron-resonance MS | Able to detect 91% of known transthyretin mutations due to high mass accuracy |
Lavatelli et al. [47] | Serum | Immunopurification, SDS-PAGE or 2DE, MS | Can detect posttranslational modifications |
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Antibody-free serum or tissue extract analysis Advantages: Identify mutations on known amyloid proteins; Measure relative abundance of mutant to wide type proteins. Disadvantages: Only applicable to known amyloid protein. | Kishikawa et al. [48] | Serum | Multidimensional liquid chromatography, ESI-MS | Applied to serum samples without requiring specific antibodies |
da Costa et al. [49] | Serum | SDS-PAGE fractionation, MALDI-Fourier transform ion cyclotron resonance MS | Quantitation of mutant to wild type transthyretin |
Ueda et al. [50] | Tissue and serum | HPLC separation, SELDI-TOF | Quantitation of mutant to wild type transthyretin within 3 hours |
Lavatelli et al. [25] | Fine needle aspiration of abdominal adipose tissue | 2DE, PMF by MALDI-TOF | Identification of amyloidogenic proteins |
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Direct extraction from FFPE samples Advantages: Identify unknown amyloid proteins in tissue sections or fat aspirates. Disadvantages: Protein extraction requires days. | Murphy et al. [11] | FFPE | HPLC purification, N-terminal sequencing, PMF | Successful identification |
Murphy et al. [51] | FFPE | HPLC, MS/MS de novo sequencing | Successful identification |
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LMD with LC-MS/MS Advantages: Capture specific regions of interest: amyloid deposits from FFPE sections; Identify unknown amyloid proteins in tissue sections; Protein extraction within hours. Disadvantages: Requires specialist LMD equipment and expertise. | Rodrigues et al. [52] | FFPE of immunoglobulin deposits in nerve tissue | LMD, LC-MS/MS | Successful identification |
Vrana et al. [55] | FFPE samples of four amyloid types, 50 cases in training set, 41 cases in validation set | LMD, LC-MS/MS, algorithm to assign amyloid type according to highest number of spectra | >98% specificity and sensitivity for the 4 amyloid types examined |
Klein et al. [53] | FFPE of various amyloid types in nerve tissue | LMD, LC-MS/MS | Successful identification of all 21 cases including transthyretin mutations |
Sethi et al. [54] | FFPE of immunoglobulin renal deposits | LMD, LC-MS/MS | Successful identification |
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MS Imaging Advantages: Detecting amyloids in situ, allowing correlation to deposits; No extraction steps. Disadvantages: Specialist MS imaging software and expertise required. | Stoeckli et al. [58] | Frozen tissue | MSI | Localization of amyloid β peptides in mouse brain sections |
Seely and Caprioli [59] | One 100 year old amyloid FFPE sample | In-situ tryptic digest and imaging MALDI-MS/MS | Successful identification of serum amyloid A |
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