Fossil remains have recently been the focus of considerable attention due to several independent reports of protein and soft-tissue preservation in ancient biological remains. The fossil whales from the Pisco Formation in Peru were previously reported to be very well preserved. A considerable percentage of these whales have their bones still articulated, and not a few have fossil baleen in life position. In this study we assayed bone samples from some fossil whales for ultrastructure preservation and the presence of original protein/proteinaceous materials. For analysis of fine details of structural preservation we used light microscopy and Scanning Electron Microscopy (SEM). The microscopy results indicated a surprising preservation of both blood vessel and osteocyte shaped structures. For protein/peptide verification we used Micro-Bicinchoninic Acid (BCA) assay for total protein determination, and Fast Performance Liquid Chromatography (FPLC) for proteins/peptides size separation. The FPLC fractions were analyzed by Matrix-assisted Laser Desorption/ Ionization-Time of Flight (MALDI-TOF) for a more specific identification of the proteins/peptides sizes. Polyamide sheet Thin-Layer Chromatography was implemented with Dansylated fossil amino acids in order to ascertain the amino acid presence in the FPLC and the C8 Solid-phase Extraction (SPE) column elution fractions. Finally, we used Liquid Chromatography-Mass Spectrometry (LC/MS) to obtain the fragmentation pattern of the peptides present in the fossil sample. The LC/MS fragmentation pattern from fossil material did not show any matching sequence when compared to trypsin digested peptide patterns in the public databases. Nevertheless, it showed secondary fragmentation patterns (MS/MS) characteristic of peptidic material, which implies that it is composed of peptides, but these simply were not cleaved by trypsin, but rather by random (probably unknown) processes. Preliminary DE NOVO sequencing attempts showed that most of the putative peptides in the samples are fragmented, with low molecular weight, but there was also some evidence of higher molecular weight material. Future research is needed in order to determine the protein identification by means of DE NOVO sequencing, and the degree of its preservation in these fossil whales.

LLU Discipline



Earth and Biological Sciences


School of Science and Technology

First Advisor

Brand, Leonard R.

Degree Name

Master of Science (MS)

Degree Level


Year Degree Awarded

January 2010

Date (Title Page)




Library of Congress/MESH Subject Headings

Whales; Fossils; Pisco Formation, Peru;



Page Count

187 p.

Digital Format


Digital Publisher

Loma Linda University Libraries

Usage Rights

This title appears here courtesy of the author, who has granted Loma Linda University a limited, non-exclusive right to make this publication available to the public. The author retains all other copyrights.


Loma Linda University Electronic Theses & Dissertations

Collection Website



Loma Linda University. Del E. Webb Memorial Library. University Archives

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