Table 2.

Summary of recent reports on the use of proteomics techniques for amyloidosis typing. Studies are grouped according to broad methodological categories.

	Investigators	Sample type	Proteomics techniques	Outcome
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
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
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
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
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