Additional file 1 of Effect of dynamic exclusion and the use of FAIMS, DIA and MALDI-mass spectrometry imaging with ion mobility on amyloid protein identification
Creators: name: Aguilan, Jennifer T.
name: Lim, Jihyeon
name: Racine-Brzostek, Sabrina
name: Fischer, Joshua
name: Silvescu, Cristina
name: Cornett, Shannon
name: Nieves, Edward
name: Mendu, Damodara Rao
name: Aliste, Carlos-Madrid
name: Semple, Stacia
name: Angeletti, Ruth
name: Weiss, Louis M.
name: Cole, Adam
name: Prystowsky, Michael
name: Pullman, James
name: Sidoli, Simone
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Infectious Diseases
subject: FOS: Health sciences

description: Supplementary Material 1. Fig S1. Table of proteins identified using Scaffold software. Transthyretin amyloid protein was identified marked with yellow star. Amyloid associated proteins such as Serum amyloid P component and Apolipoprotein E are also marked with yellow star. The total spectral counts for each sample are shown as the numbers shaded in green. Fig. 2 A. Amyloidosis sub-types from tissue specimens analyzed by LMD/LC–MS/MS. B. Total spectral counts for transthyretin protein from CR (+) ATTR-H-8 specimens with and without FAIMS (± FAIMS) with no dynamic exclusion (−DE) C. Total spectral counts for transthyretin protein from CR (+) ATTR-H-8 specimens with and without FAIMS (± FAIMS) with and without dynamic exclusion (± DE). D. Total number of proteins identified from CR (+) ATTR-H-8 specimens with and without FAIMS (± FAIMS) with no dynamic exclusion (−DE). E. Total number of proteins identified from CR (+) ATTR-H-8 specimens with and without FAIMS (± FAIMS) with and without dynamic exclusion (± DE). All the MS data acquired with or without FAIMS (± FAIMS) and with or without dynamic exclusion (± DE) were done on the Exploris 480 Orbitrap mass spectrometer. Figure S3 A. Mascot search result using error tolerant search for the transthyretin peptide YTIAALLSPYSYSTTAV(V + 14)TNPK with Val- &gt; Xle variant a + 14.0156 mass shift; B. Mascot search results with matches to query with site analysis between Val17 and Val18; C. MS/MS fragmentation for confirmation of Val- &gt; Xle substitution on Val18; D. Mascot search result re-processed in Scaffold with MS/MS fragmentation and assignments from wild type versus sequent variant transthyretin peptide. Figure S4A. PEAKS PTM and SPIDER assignment of V122I/L by V- &gt; Leu (Xle) with + 14.02 mass shift on peptide RYTIAALLSPYSTTAVVTNPKE; S5B. Methylation on peptide RYTIAALLSPYSTTAVVTNPKE; S5C. both V- &gt; Leu (Xle) and methylation on RYTIAALLSPYSTTAVVTNPKE. Figure S5. On-tissue trypsin digestion of FFPE heart tissue from A. Congo red positive (CR+) and B. Congo red negative (CR−) biopsy specimen; C. Congo red positive (CR+) and D. Congo red negative (CR−) biopsy specimen; E. in-solution trypsin digestion of a transthyretin protein standard. Figure S6. Peptide GSPAINVAVHVFR (m/z 1366.7) as potential biomarker for transthyretin observed only in A. Congo red positive heart biopsy (ATTR-H-4), C. transthyretin protein standard (TTR-Std-2) and D. Congo red positive heart autopsy (ATTR-H-9) but not in the B. Congo red negative heart biopsy (CRN-H-2) and E. Congo red negative heart autopsy specimen (CRN-H-1). Fig. S7. Principal component analysis of Congo red negative biopsy specimen (CRN-H-2) versus Congo red positive specimen (ATTR-H-4)