Evaluated Reference MS/MS Spectra Libraries

Current and Future NIST Programs

NIST/EPA/NIH Library of EI Mass Spectra

Search Program/Algorithms

Archive ProgramComputer Assisted Evaluation

NIST MS/MS Library

• June 2005 - 5,191 Spectra– 1,920 Precursor ions (incl. 292 Anions)

• From NIST, Contributors and literature• Ion trap, Triple Quad, …• New data structure/software

– Energy and precursor ion variations– Evaluation/Search logic– Range of Energies (collision cell)

Archive Program – MS/MS Mode

Archive Program + MS Interpreter

NIST MS Search Program – MS/MS Library

MW /

Formula /

Name /

Conditions

Levels

NIST Library of Peptide Ion Fragmentation Spectra

• Peptide sequences are used to infer proteins – from protein digests

• Derived from ‘Shotgun’ proteomics– Identifications originate from sequence-based search

method

• Human, Yeast, Selected Proteins, …– 90,000 Consensus spectra

• Ion trap and qtof spectra (tof/tof soon) of ESI and MALDI generated ions

Processing Pipeline

• From Raw data to Identified Proteins– Complex series of data transformations– Peptide sequences are identified by matching

m/z values against all possible sequences

• Consensus spectra extracted from pipeline– New QA/QC methods

• Library re-inserted to pipeline for faster, more reliable, more sensitive IDs

Input list

Matching peptide and probability scores

Reference spectrum and annotation

Query MS/MSHead to tail sample and reference spectra comparison

Fragmentation depends on energy/time

• FT-ICR– Lowest energies (SORI, IRMPD, SID, …)

• Ion Trap– Allows multiple stages of fragmentation

• Collision cell (Low E)– Dissociation increases with energy

• PSD – Low energy, limited energy/time

• Collision cell (High E)– Single collision, wide E distribution