Attribute	Manifest Name	Description	Required	Conditional If	Data Type	Valid Values
Filename	Mass Spectrometry Level 1,Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4,Mass Spectrometry Auxiliary File	Name of a file	True		String	
File Format	Mass Spectrometry Level 1,Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4,Mass Spectrometry Auxiliary File	Format of a file (e.g. txt, csv, fastq, bam, etc.)	True		String	hdf5 bedgraph idx idat bam bai excel powerpoint tif tiff OME-TIFF png doc pdf fasta fastq sam vcf bcf maf bed chp cel sif tsv csv txt plink bigwig wiggle gct bgzip zip seg html mov hyperlink svs Md flagstat gtf raw msf rmd bed narrowPeak bed broadPeak bed gappedPeak avi pzfx fig xml tar R script abf bpm dat jpg locs Sentrix descriptor file Python script sav gzip sdf RData hic ab1 7z gff3 json sqlite svg sra recal tranches mtx tagAlign dup DICOM czi mex cloupe Am cell am mpg M mzML scn dcc rcc pkc sf bedpe
HTAN Parent Biospecimen ID	Mass Spectrometry Level 1,Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4	HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated	True	Is lowest level is "Yes - Is lowest level"	String	
HTAN Data File ID	Mass Spectrometry Level 1,Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4,Mass Spectrometry Auxiliary File	Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)	True		String	
MS Batch ID	Mass Spectrometry Level 1	Batch ID indicating a set of samples that were run together.	True		String	
MS-based Assay Type	Mass Spectrometry Level 1	Analytes are the target molecules being measured with the assay.	True		String	LC-MS MS TMT LC-MS/MS
Analyte Type	Mass Spectrometry Level 1	The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen	True	Biospecimen is "Analyte"	String	cfDNA Analyte DNA Analyte RNA Analyte Total RNA Analyte Tissue Block Analyte Tissue Section Analyte PBMCs or Plasma or Serum Analyte cDNA Libraries Analyte PBMCs Plasma Serum Analyte lipid protein metabolite
MS-based Targeted	Mass Spectrometry Level 1	Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.	True		String	Targeted Untargeted
MS Instrument Vendor and Model	Mass Spectrometry Level 1	An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.	True		String	
MS Source	Mass Spectrometry Level 1	The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)	True		String	MALDI MALDI-2 DESI SIMS nESI Other
Polarity	Mass Spectrometry Level 1	The polarity of the mass analysis (positive or negative ion modes)	True		String	positive negative
Mass Range Low Value	Mass Spectrometry Level 1	The low value of the scanned mass range for MS1 in m/z.	True		String	
Mass Range High Value	Mass Spectrometry Level 1	The high value of the scanned mass range for MS1 in m/z.	True		String	
Data Collection Mode	Mass Spectrometry Level 1	Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.	True		String	DDA DIA Other
MS Scan Mode	Mass Spectrometry Level 1	Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)	True		String	MS MS/MS MS3 Other
MS Labeling	Mass Spectrometry Level 1	Indicates whether samples were labeled prior to MS analysis (e.g., TMT)	True		String	
Protocol Link	Mass Spectrometry Level 1	Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.	True		String	
LC Instrument Vendor and Model	Mass Spectrometry Level 1	The manufacturer of the instrument used for LC.	True		String	
LC Column Vendor and Model	Mass Spectrometry Level 1	The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'	True		String	
LC Resin	Mass Spectrometry Level 1	Details of the resin used for lc, including vendor, particle size, pore size	True		String	
LC Length Value	Mass Spectrometry Level 1	LC column length in cm.	True		String	
LC Temp Value	Mass Spectrometry Level 1	LC temperature in C.	True		String	
LC ID Value	Mass Spectrometry Level 1	LC column inner diameter in microns.	True		String	
LC Flow Rate	Mass Spectrometry Level 1	LC flow rate in nL/min.	True		String	
LC Gradient	Mass Spectrometry Level 1	The program dictates the mobile phase solvent composition over the course of the chromatographic run.	True		String	
LC Mobile Phase A	Mass Spectrometry Level 1	Composition of mobile phase A	True		String	
LC Mobile Phase B	Mass Spectrometry Level 1	Composition of mobile phase B	True		String	
Software and Version	Mass Spectrometry Level 1,Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4	Name of software used to generate expression values. String	True	Pseudo Alignment Used is "Yes - Pseudo Alignment Used"	String	
MS Instrument Metadata File	Mass Spectrometry Level 1	Additional file containing instrument metadata details. Use either synapse_path or entity_Id	False		String	
HTAN Parent Data File ID	Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4,Mass Spectrometry Auxiliary File	HTAN Data File Identifier indicating the file(s) from which these files were derived	True		String	
MS Assay Category	Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4	Type of Mass Spectrometry performed.	True		String	
Mass Spectrometry Auxiliary File	Mass Spectrometry Level 2,Mass Spectrometry Level 3,Mass Spectrometry Level 4	Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).	False		String