Peptide location fingerprinting reveals modification‐associated biomarker candidates of ageing in human tissue proteomes

Abstract

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Peptide Location Fingerprinting Reveals Tissue Region-specific Differences in Protein Structures in an Ageing Human Organ

“…Peptide location fingerprinting (PLF) is a new computational technique capable of identifying proteins exhibiting structural differences in mass spectrometry (MS) datasets derived from complex biological samples regardless of the causal mechanisms [25]. In standard proteomics, proteins are exposed to enzymes (e.g.…”

“…PLF relies on the fact that, for a given protein, the pattern of peptides detected by LC-MS/MS following protease digestion is determined by its higher order structure and reflects its solubility, stability and enzyme susceptibility. Therefore, differences in protein structure, due to either the accumulation of damage (via ageing and disease), changes in interaction states with other protein or differential synthesis, may be detected by PLF [25][26][27]. This is particularly true for the highly insoluble ECM proteins which exist within tightly bound networks.…”

“…In standard LC-MS/MS, peptides are mapped to proteins enabling quantification of protein abundance. PLF maps and quantifies peptides (by spectral counting) within specific protein regions instead, enabling the detection of statistical differences along the primary structure (peptide yield patterns) [25,26]. Previously, we have used PLF to reproducibly detect UVR-induced damage within the structures of photosensitive skin ECM proteins, in vitro [26] and tissue-specific differences in eye (ciliary zonule) and skin fibrillin-1 [27].…”

“…Previously, we have used PLF to reproducibly detect UVR-induced damage within the structures of photosensitive skin ECM proteins, in vitro [26] and tissue-specific differences in eye (ciliary zonule) and skin fibrillin-1 [27]. Crucially, and most recently, we have developed and employed an online webtool (MPLF) to identify potential biomarker proteins with structural differences between photoaged and photo-protected skin and young and aged tendon [25]. Comparisons with conventional protein quantification also revealed that PLF identifies significant differences which are unique to the methodology, particularly in ECM proteins, demonstrating that modifications to protein structure may not correlate with protein abundance in damage-susceptible long-lived proteins [25].…”

“…Although this proteomic study was highly detailed, modification-related differences to ECM protein structures were not interrogated. Since degeneration in the ageing disc is profoundly regional [8,9], and PLF can be applied post hoc to historical LC-MS/MS data (as shown for aging tendon [25]), further analysis of the DIPPER dataset presents us with a timely opportunity to test: i) the hypothesis that protein structures (as indicated by peptide yield pattern) are spatially-and potentially age-dependent in the IVD and ii) the ability of PLF to detect protein structural differences within localised tissue regions.…”