Output Formats

QuantifiedPeaks

Output where each row represents a peak trace identified by FlashLFQ. The same peptide may be detected in multiple peaks in the same file

Column Descriptions

• File Name – Name of the file from which the data was obtained.
• Base Sequence – The peptide sequence without modifications.
• Full Sequence – The peptide sequence with modifications, if any.
• Protein Group – List of protein accession numbers associated with the peptide.
• Organism – The organism from which the protein originates.
• Peptide Monoisotopic Mass – The calculated monoisotopic mass of the peptide.
• MS2 Retention Time – The retention time in seconds of the peptide's MS2 ID (PSM). Blank for PIP peak traces
• Precursor Charge – The charge state of the precursor ion that was selected for MS2.
• Theoretical MZ – The calculated mass-to-charge (m/z) ratio of the peptide precursor.
• Peak Intensity – The intensity of the detected peak. Calculated by summing the intensities of the isotope peaks in the apex (highest intensity) scan.
• Peak RT Start – The retention time at which the peak starts.
• Peak RT Apex – The retention time at which the peak reaches its highest intensity.
• Peak RT End – The retention time at which the peak ends.
• Peak MZ – The observed mass-to-charge ratio of the detected peak.
• Peak Charge – The highest intensity charge state of the detected peak.
• Num Charge States Observed – The number of different charge states detected for the peptide.
• Peak Detection Type – The method used to detect the peak (e.g., MSMS, MBR).
• PIP Q-Value – The Q-Value for peaks identified using peptide-identity-propagation (PIP, synonymous with MBR). Blank if the peptide detection type is MSMS
• PIP PEP – The posterior error probability (PEP) based Q-value for peaks that were identified using PIP. Ranges from 0-1, with lower scores indicating a higher quality PIP transfer. Blank if the peptide detection type is MSMS
• PSMs Mapped – The number of peptide-spectrum matches mapped to this peak
• Base Sequences Mapped – The number of base sequences mapped to this peak
• Full Sequences Mapped – The number of full sequences mapped to this peak
• Peak Split Valley RT – The retention time at which a peak split occurs.
• Peak Apex Mass Error (ppm) – The mass error in parts per million (ppm) of the most-abundant isotope peak at the peak apex.
• Decoy Peptide – A flag indicating whether the peptide is from a decoy database (True/False).
• Random RT – A flag indicating if the retention time assignment used for PIP was random (True/False). 'True' indicates that this was a peak-decoy used for calculating PIP Q-Values

QuantifiedPeptides

Output where each row represents a different peptide. Columns contains descriptions about the intensity of the peptide in each biological replicate/file

Column Descriptions

• Sequence – The full peptide sequence.
• Base Sequence – The peptide sequence without modifications.
• Protein Groups – List of protein accession numbers associated with the peptide.
• Gene Names – Names of the genes associated with the proteins.
• Organism – The organism from which the protein originates.
• Intensity_<Sample_Name> – The measured intensity of the peptide in a specific sample. Each column corresponds to a different biorep.
• Detection Type_<Sample_Name> – The method of detection used for the peptide in a specific sample (e.g., MSMS, 'MBR').

Each Intensity_<Sample_Name> and Detection Type_<Sample_Name> column corresponds to a specific experiment or replicate, providing quantitative and qualitative data for peptide identification and analysis.

A detection type of MSMSAmbiguousPeakFinding indicates that multiple peptides were mapped to the same peak trace and thus couldn't be quantified.

QuantifiedProteins

Output file where each row represents the quantification results for a different protein

Column Descriptions

• Protein Groups – List of protein accession numbers associated with the protein.
• Gene Name – The gene name associated with the protein.
• Organism – The organism from which the protein originates.
• Intensity_<Sample_Name> – The measured intensity of the protein in a specific sample. Each column corresponds to a different sample.

Each Intensity_<Sample_Name> column corresponds to a specific biological replicate (biorep), providing quantitative data for protein analysis