Peptide mass fingerprinting (PMF) is a technique for rapid protein identification that involves cleaving proteins into smaller peptides and measuring their masses with mass spectrometers like MALDI-TOF or ESI-TOF. The measured peptide masses are compared against known protein databases to find matches, making it faster than de novo sequencing. However, PMF is best suited for isolated proteins, as mixtures require additional MS/MS analysis for accurate identification.

1. peptide mass fingerprinting analysis
• Creative Proteomics provides peptide mass fingerprinting analysis(PMF) analysis and ions searching
against database for rapid identification of proteins.
• Peptide mass fingerprinting (PMF) is an analytical technique for protein identification. Basically, the
unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be
accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. Then these masses
are compared to either a database containing known protein sequences or even the genome
sequence which can be translated into proteins through computer programs. Then the absolute
masses of the peptides from each protein are calculated theoretically for mass comparison
between the peptides of the unknown protein and the theoretical peptide masses of each protein
to find the best match.
• The advantage of PMF method is that only the masses of the peptides is need to be known, while
time-consuming de novo peptide sequencing is then unnecessary, as long as the protein sequence
is present in the database of interest. Additionally, most PMF algorithms assume that the peptides
come from a single protein while the presence of a mixture can significantly complicate the analysis
and potentially compromise the results, thus an isolated protein is needed for the PMF based
protein identification. Mixtures exceeding a number of 2-3 proteins typically require the additional
use of MS/MS based protein identification to achieve sufficient specificity of identification.
• In sample preparation for PMF, protein samples can be derived from SDS-PAGE and then subject to
some chemical modifications. Disulfide bridges in proteins are reduced and cysteine amino acids
are carbamidomethylated chemically or acrylamidated during the gel electrophoresis. Then the
proteins are cut into several fragments using proteolytic enzymes to generate peptides for mass
spectrometric analysis.
• The digested protein can be analyzed with different types of mass spectrometers such as ESI-TOF or
MALDI-TOF. MALDI-TOF is often the preferred instrument because it allows a high sample
throughput and several proteins can be analyzed in a single experiment, if complemented by
MS/MS analysis.