With stable isotope labeling, one sample is derivatized with a “light” version of a chemical tag while another sample is labeled with a version of the same tag that incorporates a “heavy” isotope. The samples are then mixed together and analyzed in the same experiment. Identical compounds from the different samples co-elute as pairs of peaks and can be distinguished by the mass difference between the heavy and light isotope labels. Quantitation is performed on the pairs of peaks in the MS data and identification is performed using the MS/MS fragment data. This technique eliminates much of the bias that can be introduced when comparing peaks between different experiments since the data from all samples are collected within the same experiment.
Isotope coded affinity tags ICAT and Stable Isotope Labeling by Amino Acids in Cell Culture, or SILAC, are technologies that provide a mass difference in the molecular weights of differentially labeled peptides, which increases the complexity in the MS space and limits to comparing only 2 or 3 sample types.
Tandem Mass Tags (TMT and iTRAQ) are isobaric multiplexing tags. All versions of each tag have the same molecular mass but the positions of heavy and light isotopes are adjusted in order to affect the mass of a “reporter ion” region and “balance mass” region within the compound. Since all versions of the reagent tag are identical in molecular weight, the same peptides originating from different samples will have the same mass in MS space regardless of which reporter ion is attached. Upon fragmentation, the reporter ion can be clearly distinguished, and the identity of the peptide determined from the sequence of the larger MS/MS peptide fragments, and the quantity of that peptide from each biological sample determined from the areas of each respective reporter ion peak.

TMT, Tandem Mass Tag

Unimod links

• UNIMOD TMT 2-plex link
• UNIMOD TMT 6-plex link
• UNIMOD cysTMT 6-plex link
• UNIMOD iodoTMT 6-plex link
• UNIMOD TMTpro_zero link
• UNIMOD TMTpro 16-plex link
• UNIMOD TMTpro 18-plex link
• UNIMOD TMTpro super heavy link

iTRAQ

There are multiple different kits available, including bulk etc. shop around. The iTRAQ 4-plex kits are simply called iTRAQ without the designation as to 4-plex or 8-plex, as the original kits were all 4-plex so they didn’t need to differentiate. With the inception of 8-plex they had to add the “8-plex” terminology to the kits.

iTRAQ 4-plex 4352135 from Sigma,
iTRAQ 8-plex 4381662 from Sigma,
iTRAQ Reagents from Sigma
iTRAQ Reagents from Sciex

What is the mass added to the peptide for iTRAQ 4plex and 8plex? from the FAQ's at the Sciex site.
The table below list the masses added to the peptides per amine (N-term and Lys residues) as well as the reporter fragment m/z seen by MSMS analysis.

Unimod links

• UNIMOD iTRAQ 8-plex 113, 114, 116, 117 link
• UNIMOD iTRAQ 8-plex 115, 118, 119, 121 link
• UNIMOD iTRAQ 4-plex 114 link
• UNIMOD iTRAQ 4-plex 115 link
• UNIMOD iTRAQ 4-plex 116, 117 link

SILAC Metabolic Labeling Systems

• Pino et al combined SILAC with DIA quantification workflows, see Ref 7
• Protocols from ShaoEn Ong and Matthias Mann A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC) Ref 8

There are multiple different kits from different vendors available:

SILAC systems from Thermo
search SILAC to find related products from Sigma
SILAC Kits and Reagents from Cambridge Isotope Laboratories
there are likely other I missed, so do your homework..

• The Trans-Proteomic Pipeline (TPP) is a complete and mature suite of free and open-source software tools for MS data representation, MS data visualization, peptide identification and validation, protein identification, quantification, and annotation, data storage and mining, and biological inference. The Automated Statistical Analysis on Protein Ratio (ASAPRatio) and XPRESS software tools are part of the TPP calculates the relative abundance of proteins, such as those obtained from stable isotope labeled precursors, by reconstructing the light and heavy elution profiles of the precursor ions and determining the elution areas of each peak
  
  
• Skyline is also being used to integrate SILAC data.
  Check Skyline Webinar 12: Isotope Labeled Standards in Skyline for more information
  You may need to define a new Isotope Label Type: Click the "Isotope label type" dropdown list in the Peptide Settings - Modifications tab, and click the <Edit list...> element. Then specify your isotope label types in a line separated list in the form that appears. Once you have your two label types, you need to make sure that Arg10, Lys8 are checked when you have "heavy" selected in the list, and Arg6, Lys4 are checked when you have "medium" selected. All of these modifications will need to be added to the "Isotope modifications" list. The "Internal standard type" list will change to a check list (from a dropdown list), which allows you to specify multiple internal standard types. You would just make sure nothing is checked in this list for a SILAC experiment, which is the equivalent to "None" in the dropdown list. For targeted proteomics experiments for sample preparations involving both AQUA labeled peptides and 15N labeled proteins, both get checked as internal standard types.
  
  
• MaxQuant
  MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. MaxQuant is freely available and can be downloaded from this site.
  MaxQuant quantitative proteomics software package
• Perseus
  for interpreting protein quantification, interaction and post-translational modification data
  
  
• PEAKS Q (limited free trial)
  PEAKS Q SILAC Quantification Algorithms
  

AQUA or Absolute QUAntitation

There are multiple vendors that provide AQUA peptides:

AQUA peptides from Sigma
Peptides for Targeted Quantitation from Thermo
PeptiQuant Assay Kits from Cambridge Isotope Laboratories
there are likely other I missed, so do your homework..

Data analysis
You can use Skyline to estimate the absolute molecular quantities of peptides in your experiments.
Absolute Quantification Tutorial
Webinar #13: Calibrated Quantification with Skyline

Heavy labeled protein standards

There are multiple vendors that provide heavy labeled proteins:

Heavy-Labeled MS Proteins Standards from Cambridge Isotope Laboratories
SILu Prot Protein Standards for Quantitative Mass Spectrometry from Sigma
1-Step Heavy Protein IVT Kit from Thermo
there are likely other I missed, so do your homework..

Chemical labeling

References

TMT labeling workflow
1. Tandem Mass Tag (TMT) Labeling Workflow Renny Lan, IDeA National Resource for Proteomics Workshop for Core Directors and Staff link (pdf)

TMT labeling of small amounts of peptides
2. Sample Preparation for Relative Quantitation of Proteins Using Tandem Mass Tags (TMT) and Mass Spectrometry (MS) Erdjument-Bromage H, Huang FK, Neubert TA. Methods Mol Biol. 2018;1741:135-149. doi: 10.1007/978-1-4939-7659-1_11. link

TMTpro
3. TMTpro Reagents: A Set of Isobaric Labeling Mass Tags Enables Simultaneous Proteome-Wide Measurements Across 16 Samples Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, Paulo JA. Nat Methods. 2020 Apr;17(4):399-404. doi: 10.1038/s41592-020-0781-4. Epub 2020 Mar 16. link
4. TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I. Nat Methods. 2020 Apr;17(4):399-404. doi: 10.1038/s41592-020-0781-4. Epub 2020 Mar 16. link
5. A Triple Knockout Isobaric-Labeling Quality Control Platform With an Integrated Online Database Search Gygi JP, Ramin Rad, Navarrete-Perea J, Younesi S, Gygi SP, Paulo JA. Nat Methods. 2020 Apr;17(4):399-404. doi: 10.1038/s41592-020-0781-4. Epub 2020 Mar 16. link
6. TMTpro: Best Practices
   Tony Herren, PhD, Field Application Scientist – Proteomics/Mass Spectrometry link (pdf)

SILAC
7. Improved SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradation Pino LK, Baeza J, Lauman R, Schilling B, Garcia BA. J Proteome Res. 2021 Apr 2;20(4):1918-1927. doi: 10.1021/acs.jproteome.0c00938. Epub 2021 Mar 25. link
8. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Mol Cell Proteomics. 2002 May;1(5):376-86. doi: 10.1074/mcp.m200025-mcp200. link
9. Comparing SILAC- and stable isotope dimethyl-labeling approaches for quantitative proteomics. Lau HT, Suh HW, Golkowski M, Ong SE. J Proteome Res. 2014 Sep 5;13(9):4164-74. doi: 10.1021/pr500630a. Epub 2014 Aug 12. link
10. An Overview of Advanced SILAC-Labeling Strategies for Quantitative Proteomics Terzi F, Cambridge S. Methods Enzymol. 2017;585:29-47. doi: 10.1016/bs.mie.2016.09.014. Epub 2017 Jan 12. link

AQUA and Heavy labeled protein standards

11. Multiple-Reaction Monitoring-Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures. Hoofnagle AN, Becker JO, Oda MN, Cavigiolio G, Mayer P, Vaisar T. Clin Chem. 2012 Apr;58(4):777-81. Epub 2012 Feb 3. link

Chemical labeling

12. Multiplex Peptide Stable Isotope Dimethyl Labeling for Quantitative Proteomics Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ. Nat Protoc. 2009;4(4):484-94. doi: 10.1038/nprot.2009.21. link
13. Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Boersema PJ, Aye TT, van Veen TA, Heck AJ, Mohammed S. Proteomics. 2008 Nov;8(22):4624-32. doi: 10.1002/pmic.200800297. link
14. Differential Stable Isotope Labeling of Peptides for Quantitation and De Novo Sequence Derivation Goodlett DR, Keller A, Watts JD, Newitt R, Yi EC, Purvine S, Eng JK, von Haller P, Aebersold R, Kolker E. Rapid Commun Mass Spectrom. 2001;15(14):1214-21. doi: 10.1002/rcm.362. link