column Header 	Description
filename	MS/MS spectrum identifier (runName.firstScanNum.lastScanNum.parentCharge) when firstScanNum and lastScanNum are different, multiple MS/MS spectra have been merged that were acquired nearby in chromatographic time 
parent_charge	Charge of precursor ion
score	Spectrum Mill identification score    
deltaForwardReverseScore	The difference between Spectrum Mill identification score of the best target peptide (forward peptide sequence) and decoy peptide (reversed peptide sequence). A value less than or equal to zero indicates a likely false-positive identification.
deltaRank1Rank2Score	The difference between Spectrum Mill identification score of the rank1 and rank2 target peptides (forward peptide sequence).
percent_scored_peak_intensity	Percent of product ion intensity (after peak detection) that is matched to a scored ion type
totalIntensity	Chromatographic peak are of precursor ion and its isotopes
variableSites	The amino acid position in the protein sequence from accession_number of a modified amino acid indicated in lowercase. 
nterm	Name of modification at peptide N-terminus (ex: iTRAQ, Acetyl,Hydrogen)
StartAA	The amino acid position in the protein sequence of the first amino acid in the peptide
previous_aa	Amino acid preceding the sequence in accession_number , (-) indicates N-terminus of protein
sequence	Peptide sequence -lower case indicates variable modification
next_aa	Amino acid following the sequence in accession_number , (-) indicates C-terminus of protein
modifications	Amino acid modified: name of modification (Ex: K:iTRAQ, K:iTRAQ-Lys-Only, C:Carbamidomethylation, c:Pyro Carbamidomethyl Cys, q:Pyroglutamic acid, m:Oxidized methionine, n:Deamidated)
iTRAQ_114_117	Ratio iTRAQ_114 intensity / iTRAQ_117 intensity, not log2, not normalized, not isotope corrected
iTRAQ_115_117	Ratio iTRAQ_115 intensity / iTRAQ_117 intensity, not log2, not normalized, not isotope corrected
iTRAQ_116_117	Ratio iTRAQ_115 intensity / iTRAQ_117 intensity, not log2, not normalized, not isotope corrected
iTRAQ_114	iTRAQ_114 intensity, not normalized, not isotope corrected
iTRAQ_115	iTRAQ_115 intensity, not normalized, not isotope corrected
iTRAQ_116	iTRAQ_116 intensity, not normalized, not isotope corrected
iTRAQ_117	iTRAQ_117 intensity, not normalized, not isotope corrected
precursorAveragineChiSquared	1-Chi2 measure of the precursor ion isotope cluster shape (combined from the 2 MS1 scans immediately before and after the MS2 scan) as compared to the theoretical isotpe cluster shape of averagine. (0.85 to 1.0 is good)
precursorIsolationPurityPercent	The intensity of the precursor ion and its isotopes divided by the total peak inensity in the precursor isolation window used for the MS2 scan (combined from the 2 MS1 scans immediately before and after the MS2 scan), <50% means reporter quantitation was not used because of expected contamination by co-fragmented peptides.
precursorIsolationIntensity	The denominator used in the precursorIsolationPurity metric
ratioReporterIonToPrecursor	Sum of the reporter ion intensities (iTRAQ_114+iTRAQ_115+iTRAQ_116+iTRAQ_117) divided by precursorIsolationIntensity
retentionTimeMin	Time from the start of the LC gradient to the chromatographic apex of the precursor ion
chromatographicPeakWidthSec	Width of  precursor ion chromatographic peak, 0 means no more than 1 MS 1 scan had a satisfactory precursor isotope cluster shape
parent_m_over_z	measured precursor m/z
matched_parent_mass	calculated mass of peptide MH+ in database before accounting for variable modifications
delta_parent_mass	Difference in measured parent mass (Da) of identified peptide and calculated mass of peptide in database before accounting for variable modifications. +16 is consistent with oxidation.
delta_parent_mass_ppm	Difference in measured parent mass (Da) of identified peptide and calculated mass of peptide in database after accounting for variable modifications.
protein_mw	Calculated protein MW (Da) of the protein sequence belonging to accession_number
species	species parsed form FASTA file by SM (Ex: HOMO SAPIENS, MUS MUSCULUS, PIG, BOVIN, SHEEP)
accession_number	RefSeq protein ID, UniProt ID for appended labaoratory contaminants
accession_numbers	All accession numbers in the searched database containing sequence
geneSymbol	NCBI Entrez gene symbol
entry_name	Protein name from FASTA sequence database searched